Compositions and methods for the diagnosis and treatment of tumor

ABSTRACT

The present invention is directed to compositions of matter useful for the diagnosis and treatment of tumor in mammals and to methods of using those compositions of matter for the same.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.12/031,612, filed Feb. 14, 2008, which is a continuation of U.S. patentapplication Ser. No. 10/916,250, filed Aug. 11, 2004, which is acontinuation of U.S. patent application Ser. No. 10/125,166, filed Apr.17, 2002, which is a continuation-in-part of each of the followingapplications: U.S. patent application Ser. No. 09/918,585, filed Jul.30, 2001, U.S. patent application Ser. No. 09/904,553, filed Jul. 13,2001, International Patent Application Serial No. PCT/US01/06520, filedFeb. 28, 2001, U.S. patent application Ser. No. 09/665,350, filed Sep.18, 2000, International Patent Application Serial No. PCT/US00/04414,filed Feb. 22, 2000, International Patent Application Serial No.PCT/US00/04341, filed Feb. 18, 2000, International Patent ApplicationSerial No. PCT/US99/21090, filed Sep. 15, 1999, International PatentApplication Serial No. PCT/US99/05028, filed Mar. 8, 1999, InternationalPatent Application Serial No. PCT/US98/19330, filed Sep. 16, 1998, U.S.Provisional Patent Application Ser. No. 60/077,649, filed Mar. 11, 1998and U.S. Provisional Patent Application Ser. No. 60/063,542, filed Oct.28, 1997, the entire disclosures of which are hereby incorporated byreference.

FIELD OF THE INVENTION

The present invention is directed to compositions of matter useful forthe diagnosis and treatment of tumor in mammals and to methods of usingthose compositions of matter for the same.

BACKGROUND OF THE INVENTION

Malignant tumors (cancers) are the second leading cause of death in theUnited States, after heart disease (Boring et al., CA Cancel J. Clin.43:7 (1993)). Cancer is characterized by the increase in the number ofabnormal, or neoplastic, cells derived from a normal tissue whichproliferate to form a tumor mass, the invasion of adjacent tissues bythese neoplastic tumor cells, and the generation of malignant cellswhich eventually spread via the blood or lymphatic system to regionallymph nodes and to distant sites via a process called metastasis. In acancerous state, a cell proliferates under conditions in which normalcells would not grow. Cancer manifests itself in a wide variety offorms, characterized by different degrees of invasiveness andaggressiveness.

In attempts to discover effective cellular targets for cancer therapy,researchers have sought identify polypeptides that are specificallyoverexpressed on the surface of a particular type of cancer cell ascompared to on one or more normal non-cancerous cell(s). Theidentification of such tumor-associated cell surface antigenpolypeptides has given rise to the ability to specifically target cancercells for destruction via antibody-based therapies. In this regard, itis noted that antibody-based therapy has proved very effective in thetreatment of certain cancers. For example, HERCEPTIN® and RITUXAN® (bothfrom Genentech Inc., South San Francisco, Calif.) are antibodies thathave been used successfully to treat breast cancer and non-Hodgkin'slymphoma, respectively. More specifically, HERCEPTIN® is a recombinantDNA-derived humanized monoclonal antibody that selectively binds to theextracellular domain of the human epidermal growth factor receptor 2(HER2) proto-oncogene. HER2 protein overexpression is observed in 25-30%of primary breast cancers. RITUXAN® is a genetically engineered chimericmurine/human monoclonal antibody directed against the CD20 antigen foundon the surface of normal and malignant B lymphocytes. Both theseantibodies are recombinantly produced in CHO cells.

In other attempts to discover effective cellular targets for cancertherapy, researchers have sought to identify polypeptides that areproduced and secreted by a particular type of cancer cell at anexpression level that is higher than that produced and secreted by oneor more normal non-cancerous cell(s). Moreover, such polypeptides may beexpressed by cells which produce and/or secrete polypeptides having apotentiating or growth-enhancing effect on cancer cells. Such secretedfactors are often proteins that provide cancer cells with growthadvantages over normal cells and include such things as, for example,angiogenic factors, cellular adhesion factors, growth factors, and thelike. Identification of antagonists of such secreted polypeptides wouldbe expected to serve as effective therapeutic agents for the treatmentof such cancers. Furthermore, identification of the overexpression ofsuch secreted factors would be useful for the diagnosis of particularcancers in mammals.

Despite the above identified advances in mammalian cancer therapy, thereis a great need for additional diagnostic and therapeutic agents capableof detecting the presence of tumor in a mammal and for effectivelyinhibiting neoplastic cell growth, respectively. Accordingly, it is theobjective of the present invention to identify cell surface polypeptidesthat are overexpressed on certain cancer cells as compared to on normalcells or other different cancer cells, or secreted polypeptides that areoverexpressed by certain cancer cells as compared to by normal cells orother different cancer cells and/or other surrounding non-cancer cells,and to use those polypeptides, and their encoding nucleic acids, toproduce compositions of matter useful in the therapeutic treatment anddiagnostic detection of cancer in mammals.

SUMMARY OF THE INVENTION A. Embodiments

In the present specification, Applicants describe for the first time theidentification of various cellular polypeptides (and their encodingnucleic acids or fragments thereof) which are expressed to a greaterdegree on the surface of or by one or more types of cancer cell ascompared to on the surface of or by one or more types of normalnon-cancer cells. Alternatively, such polypeptides may be expressed bycells which produce and/or secrete polypeptides having a potentiating orgrowth-enhancing effect on cancer cells. Such polypeptides are hereinreferred to as Tumor-associated Antigenic Target polypeptides (“TAT”polypeptides) and are expected to serve as effective targets for cancertherapy and diagnosis in mammals.

Accordingly, in one embodiment of the present invention, the inventionprovides an isolated nucleic acid molecule comprising a nucleotidesequence that encodes a tumor-associated antigenic target polypeptide orfragment thereof (a “TAT” polypeptide).

In certain aspects, the isolated nucleic acid molecule comprises anucleotide sequence having at least about 80% nucleic acid sequenceidentity, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%nucleic acid sequence identity, to (a) a DNA molecule encoding afull-length TAT polypeptide having an amino acid sequence as disclosedherein, a TAT polypeptide amino acid sequence lacking the signal peptideas disclosed herein, an extracellular domain of a transmembrane TATpolypeptide, with or without the signal peptide, as disclosed herein orany other specifically defined fragment of a full-length TAT polypeptideamino acid sequence as disclosed herein, or (b) the complement of theDNA molecule of (a).

In other aspects, the isolated nucleic acid molecule comprises anucleotide sequence having at least about 80% nucleic acid sequenceidentity, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%nucleic acid sequence identity, to (a) a DNA molecule comprising thecoding sequence of a full-length TAT polypeptide cDNA as disclosedherein, the coding sequence of a TAT polypeptide lacking the signalpeptide as disclosed herein, the coding sequence of an extracellulardomain of a transmembrane TAT polypeptide, with or without the signalpeptide, as disclosed herein or the coding sequence of any otherspecifically defined fragment of the full-length TAT polypeptide aminoacid sequence as disclosed herein, or (b) the complement of the DNAmolecule of (a).

In further aspects, the invention concerns an isolated nucleic acidmolecule comprising a nucleotide sequence having at least about 80%nucleic acid sequence identity, alternatively at least about 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, or 99% nucleic acid sequence identity, to (a) a DNA moleculethat encodes the same mature polypeptide encoded by the full-lengthcoding sequence of any of the human protein cDNAs deposited with theATCC as disclosed herein, or (b) the complement of the DNA molecule of(a). In this regard, the term “full-length coding sequence” refers tothe TAT polypeptide-encoding nucleotide sequence of the cDNA that isinserted into the vector deposited with the ATCC (which is often shownbetween start and stop codons, inclusive thereof, in the accompanyingfigures).

Another aspect of the invention provides an isolated nucleic acidmolecule comprising a nucleotide sequence encoding a TAT polypeptidewhich is either transmembrane domain-deleted or transmembranedomain-inactivated, or is complementary to such encoding nucleotidesequence, wherein the transmembrane domain(s) of such polypeptide(s) aredisclosed herein. Therefore, soluble extracellular domains of the hereindescribed TAT polypeptides are contemplated.

In other aspects, the present invention is directed to isolated nucleicacid molecules which hybridize to (a) a nucleotide sequence encoding aTAT polypeptide having a full-length amino acid sequence as disclosedherein, a TAT polypeptide amino acid sequence lacking the signal peptideas disclosed herein, an extracellular domain of a transmembrane TATpolypeptide, with or without the signal peptide, as disclosed herein orany other specifically defined fragment of a full-length TAT polypeptideamino acid sequence as disclosed herein, or (b) the complement of thenucleotide sequence of (a). In this regard, an embodiment of the presentinvention is directed to fragments of a full-length TAT polypeptidecoding sequence, or the complement thereof, as disclosed herein, thatmay find use as, for example, hybridization probes useful as, forexample, diagnostic probes, antisense oligonucleotide probes, or forencoding fragments of a full-length TAT polypeptide that may optionallyencode a polypeptide comprising a binding site for an anti-TATpolypeptide antibody, a TAT binding oligopeptide or other small organicmolecule that binds to a TAT polypeptide. Such nucleic acid fragmentsare usually at least about 5 nucleotides in length, alternatively atleast about 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75,80, 85, 90, 95, 100, 105, 110, 115, 120, 125, 130, 135, 140, 145, 150,155, 160, 165, 170, 175, 180, 185, 190, 195, 200, 210, 220, 230, 240,250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380,390, 400, 410, 420, 430, 440, 450, 460, 470, 480, 490, 500, 510, 520,530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660,670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800,810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940,950, 960, 970, 980, 990, or 1000 nucleotides in length, wherein in thiscontext the term “about” means the referenced nucleotide sequence lengthplus or minus 10% of that referenced length. It is noted that novelfragments of a TAT polypeptide-encoding nucleotide sequence may bedetermined in a routine manner by aligning the TAT polypeptide-encodingnucleotide sequence with other known nucleotide sequences using any of anumber of well known sequence alignment programs and determining whichTAT polypeptide-encoding nucleotide sequence fragment(s) are novel. Allof such novel fragments of TAT polypeptide-encoding nucleotide sequencesare contemplated herein. Also contemplated are the TAT polypeptidefragments encoded by these nucleotide molecule fragments, preferablythose TAT polypeptide fragments that comprise a binding site for ananti-TAT antibody, a TAT binding oligopeptide or other small organicmolecule that binds to a TAT polypeptide.

In another embodiment, the invention provides isolated TAT polypeptideencoded by any of the isolated nucleic acid sequences hereinaboveidentified.

In a certain aspect, the invention concerns an isolated TAT polypeptide,comprising an amino acid sequence having at least about 80% amino acidsequence identity, alternatively at least about 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%amino acid sequence identity, to a TAT polypeptide having a full-lengthamino acid sequence as disclosed herein, a TAT polypeptide amino acidsequence lacking the signal peptide as disclosed herein, anextracellular domain of a transmembrane TAT polypeptide protein, with orwithout the signal peptide, as disclosed herein, an amino acid sequenceencoded by any of the nucleic acid sequences disclosed herein or anyother specifically defined fragment of a full-length TAT polypeptideamino acid sequence as disclosed herein.

In a further aspect, the invention concerns an isolated TAT polypeptidecomprising an amino acid sequence having at least about 80% amino acidsequence identity, alternatively at least about 81%, 82%, 83%, 84%, 85%,86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%amino acid sequence identity, to an amino acid sequence encoded by anyof the human protein cDNAs deposited with the ATCC as disclosed herein.

In a specific aspect, the invention provides an isolated TAT polypeptidewithout the N-terminal signal sequence and/or the initiating methionineand is encoded by a nucleotide sequence that encodes such an amino acidsequence as hereinbefore described. Processes for producing the same arealso herein described, wherein those processes comprise culturing a hostcell comprising a vector which comprises the appropriate encodingnucleic acid molecule under conditions suitable for expression of theTAT polypeptide and recovering the TAT polypeptide from the cellculture.

Another aspect of the invention provides an isolated TAT polypeptidewhich is either transmembrane domain-deleted or transmembranedomain-inactivated. Processes for producing the same are also hereindescribed, wherein those processes comprise culturing a host cellcomprising a vector which comprises the appropriate encoding nucleicacid molecule under conditions suitable for expression of the TATpolypeptide and recovering the TAT polypeptide from the cell culture.

In other embodiments of the present invention, the invention providesvectors comprising DNA encoding any of the herein describedpolypeptides. Host cell comprising any such vector are also provided. Byway of example, the host cells may be CHO cells, E. coli, or yeast. Aprocess for producing any of the herein described polypeptides isfurther provided and comprises culturing host cells under conditionssuitable for expression of the desired polypeptide and recovering thedesired polypeptide from the cell culture.

In other embodiments, the invention provides isolated chimericpolypeptides comprising any of the herein described TAT polypeptidesfused to a heterologous (non-TAT) polypeptide. Example of such chimericmolecules comprise any of the herein described TAT polypeptides fused toa heterologous polypeptide such as, for example, an epitope tag sequenceor a Fc region of an immunoglobulin.

In another embodiment, the invention provides an antibody which binds,preferably specifically, to any of the above or below describedpolypeptides. Optionally, the antibody is a monoclonal antibody,antibody fragment, chimeric antibody, humanized antibody, single-chainantibody or antibody that competitively inhibits the binding of ananti-TAT polypeptide antibody to its respective antigenic epitope.Antibodies of the present invention may optionally be conjugated to agrowth inhibitory agent or cytotoxic agent such as a toxin, including,for example, a maytansinoid or calicheamicin, an antibiotic, aradioactive isotope, a nucleolytic enzyme, or the like. The antibodiesof the present invention may optionally be produced in CHO cells orbacterial cells and preferably induce death of a cell to which theybind. For diagnostic purposes, the antibodies of the present inventionmay be detectably labeled, attached to a solid support, or the like.

In other embodiments of the present invention, the invention providesvectors comprising DNA encoding any of the herein described antibodies.Host cell comprising any such vector are also provided. By way ofexample, the host cells may be CHO cells, E. coli, or yeast. A processfor producing any of the herein described antibodies is further providedand comprises culturing host cells under conditions suitable forexpression of the desired antibody and recovering the desired antibodyfrom the cell culture.

In another embodiment, the invention provides oligopeptides (“TATbinding oligopeptides”) which bind, preferably specifically, to any ofthe above or below described TAT polypeptides. Optionally, the TATbinding oligopeptides of the present invention may be conjugated to agrowth inhibitory agent or cytotoxic agent such as a toxin, including,for example, a maytansinoid or calicheamicin, an antibiotic, aradioactive isotope, a nucleolytic enzyme, or the like. The TAT bindingoligopeptides of the present invention may optionally be produced in CHOcells or bacterial cells and preferably induce death of a cell to whichthey bind. For diagnostic purposes, the TAT binding oligopeptides of thepresent invention may be detectably labeled, attached to a solidsupport, or the like.

In other embodiments of the present invention, the invention providesvectors comprising DNA encoding any of the herein described TAT bindingoligopeptides. Host cell comprising any such vector are also provided.By way of example, the host cells may be CHO cells, E. coli, or yeast. Aprocess for producing any of the herein described TAT bindingoligopeptides is further provided and comprises culturing host cellsunder conditions suitable for expression of the desired oligopeptide andrecovering the desired oligopeptide from the cell culture.

In another embodiment, the invention provides small organic molecules(“TAT binding organic molecules”) which bind, preferably specifically,to any of the above or below described TAT polypeptides. Optionally, theTAT binding organic molecules of the present invention may be conjugatedto a growth inhibitory agent or cytotoxic agent such as a toxin,including, for example, a maytansinoid or calicheamicin, an antibiotic,a radioactive isotope, a nucleolytic enzyme, or the like. The TATbinding organic molecules of the present invention preferably inducedeath of a cell to which they bind. For diagnostic purposes, the TATbinding organic molecules of the present invention may be detectablylabeled, attached to a solid support, or the like.

In a still further embodiment, the invention concerns a composition ofmatter comprising a TAT polypeptide as described herein, a chimeric TATpolypeptide as described herein, an anti-TAT antibody as describedherein, a TAT binding oligopeptide as described herein, or a TAT bindingorganic molecule as described herein, in combination with a carrier.Optionally, the carrier is a pharmaceutically acceptable carrier.

In yet another embodiment, the invention concerns an article ofmanufacture comprising a container and a composition of matter containedwithin the container, wherein the composition of matter may comprise aTAT polypeptide as described herein, a chimeric TAT polypeptide asdescribed herein, an anti-TAT antibody as described herein, a TATbinding oligopeptide as described herein, or a TAT binding organicmolecule as described herein. The article may further optionallycomprise a label affixed to the container, or a package insert includedwith the container, that refers to the use of the composition of matterfor the therapeutic treatment or diagnostic detection of a tumor.

Another embodiment of the present invention is directed to the use of aTAT polypeptide as described herein, a chimeric TAT polypeptide asdescribed herein, an anti-TAT polypeptide antibody as described herein,a TAT binding oligopeptide as described herein, or a TAT binding organicmolecule as described herein, for the preparation of a medicament usefulin the treatment of a condition which is responsive to the TATpolypeptide, chimeric TAT polypeptide, anti-TAT polypeptide antibody,TAT binding oligopeptide, or TAT binding organic molecule.

B. Additional Embodiments

Another embodiment of the present invention is directed to a method forkilling a cancer cell that expresses a TAT polypeptide, wherein themethod comprises contacting the cancer cell with an antibody, anoligopeptide or a small organic molecule that binds to the TATpolypeptide, thereby resulting in the death of the cancer cell.Optionally, the antibody is a monoclonal antibody, antibody fragment,chimeric antibody, humanized antibody, or single-chain antibody.Antibodies, TAT binding oligopeptides and TAT binding organic moleculesemployed in the methods of the present invention may optionally beconjugated to a growth inhibitory agent or cytotoxic agent such as atoxin, including, for example, a maytansinoid or calicheamicin, anantibiotic, a radioactive isotope, a nucleolytic enzyme, or the like.The antibodies and TAT binding oligopeptides employed in the methods ofthe present invention may optionally be produced in CHO cells orbacterial cells.

Another embodiment of the present invention is directed to a method forinhibiting the growth of a cancer cell, wherein the growth of saidcancer cell is at least in part dependent upon the growth potentiatingeffect(s) of a TAT polypeptide, wherein the method comprises contactingthe TAT polypeptide with an antibody, an oligopeptide or a small organicmolecule that binds to the TAT polypeptide, thereby antagonizing thegrowth-potentiating activity of the TAT polypeptide and, in turn,inhibiting the growth of the cancer cell. Preferably the growth of thecancer cell is completely inhibited. Optionally, the antibody is amonoclonal antibody, antibody fragment, chimeric antibody, humanizedantibody, or single-chain antibody. Antibodies, TAT bindingoligopeptides and TAT binding organic molecules employed in the methodsof the present invention may optionally be conjugated to a growthinhibitory agent or cytotoxic agent such as a toxin, including, forexample, a maytansinoid or calicheamicin, an antibiotic, a radioactiveisotope, a nucleolytic enzyme, or the like. The antibodies and TATbinding oligopeptides employed in the methods of the present inventionmay optionally be produced in CHO cells or bacterial cells.

Yet another embodiment of the present invention is directed to a methodof therapeutically treating a TAT polypeptide-expressing tumor in amammal, wherein the method comprises administering to the mammal atherapeutically effective amount of an antibody, an oligopeptide or asmall organic molecule that binds to the TAT polypeptide, therebyresulting in the effective therapeutic treatment of the tumor.Optionally, the antibody is a monoclonal antibody, antibody fragment,chimeric antibody, humanized antibody, or single-chain antibody.Antibodies, TAT binding oligopeptides and TAT binding organic moleculesemployed in the methods of the present invention may optionally beconjugated to a growth inhibitory agent or cytotoxic agent such as atoxin, including, for example, a maytansinoid or calicheamicin, anantibiotic, a radioactive isotope, a nucleolytic enzyme, or the like.The antibodies and oligopeptides employed in the methods of the presentinvention may optionally be produced in CHO cells or bacterial cells.

Yet another embodiment of the present invention is directed to a methodof therapeutically treating a tumor in a mammal, wherein the growth ofsaid tumor is at least in part dependent upon the growth potentiatingeffect(s) of a TAT polypeptide, wherein the method comprisesadministering to the mammal a therapeutically effective amount of anantibody, an oligopeptide or a small organic molecule that binds to theTAT polypeptide, thereby antagonizing the growth potentiating activityof said TAT polypeptide and resulting in the effective therapeutictreatment of the tumor. Optionally, the antibody is a monoclonalantibody, antibody fragment, chimeric antibody, humanized antibody, orsingle-chain antibody. Antibodies, TAT binding oligopeptides and TATbinding organic molecules employed in the methods of the presentinvention may optionally be conjugated to a growth inhibitory agent orcytotoxic agent such as a toxin, including, for example, a maytansinoidor calicheamicin, an antibiotic, a radioactive isotope, a nucleolyticenzyme, or the like. The antibodies and oligopeptides employed in themethods of the present invention may optionally be produced in CHO cellsor bacterial cells.

Yet another embodiment of the present invention is directed to a methodfor treating or preventing a cell proliferative disorder associated withaltered, preferably increased, expression or activity of a TATpolypeptide, the method comprising administering to a subject in need ofsuch treatment an effective amount of an antagonist of a TATpolypeptide. Preferably, the cell proliferative disorder is cancer andthe antagonist of the TAT polypeptide is an anti-TAT polypeptideantibody, TAT binding oligopeptide, TAT binding organic molecule orantisense oligonucleotide. Effective treatment or prevention of the cellproliferative disorder may be a result of direct killing or growthinhibition of cells that express a TAT polypeptide or by antagonizingthe cell proliferative activity of a TAT polypeptide.

Yet another embodiment of the present invention is directed to a methodof determining the presence of a TAT polypeptide in a sample suspectedof containing the TAT polypeptide, wherein the method comprises exposingthe sample to an antibody, oligopeptide or small organic molecule thatbinds to the TAT polypeptide and determining binding of the antibody,oligopeptide or organic molecule to the TAT polypeptide in the sample,wherein the presence of such binding is indicative of the presence ofthe TAT polypeptide in the sample. Optionally, the sample may containcells (which may be cancer cells) suspected of expressing the TATpolypeptide. The antibody, TAT binding oligopeptide or TAT bindingorganic molecule employed in the method may optionally be detectablylabeled, attached to a solid support, or the like.

A further embodiment of the present invention is directed to a method ofdiagnosing the presence of a tumor in a mammal, wherein the methodcomprises detecting the level of expression of a gene encoding a TATpolypeptide (a) in a test sample of tissue cells obtained from saidmammal, and (b) in a control sample of known normal cells of the sametissue origin, wherein a higher level of expression of the TATpolypeptide in the test sample, as compared to the control sample, isindicative of the presence of tumor in the mammal from which the testsample was obtained.

Another embodiment of the present invention is directed to a method ofdiagnosing the presence of a tumor in a mammal, wherein the methodcomprises (a) contacting a test sample comprising tissue cells obtainedfrom the mammal with an antibody, oligopeptide or small organic moleculethat binds to a TAT polypeptide and (b) detecting the formation of acomplex between the antibody, oligopeptide or small organic molecule andthe TAT polypeptide in the test sample, wherein the formation of acomplex is indicative of the presence of a tumor in the mammal.Optionally, the antibody, TAT binding oligopeptide or TAT bindingorganic molecule employed is detectably labeled, attached to a solidsupport, or the like, and/or the test sample of tissue cells is obtainedfrom an individual suspected of having a cancerous tumor.

In yet further embodiments, the invention is directed to the followingset of potential claims for this application:

1. Isolated nucleic acid having at least 80% nucleic acid sequenceidentity to:

(a) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4);

(b) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking its associatedsignal peptide;

(c) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), withits associated signal peptide;

(d) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4),lacking its associated signal peptide;

(e) the nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQID NO:2);

(f) the full-length coding sequence of the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(g) the full-length coding sequence of the cDNA deposited under any ATCCaccession number shown in Table 7; or

(h) the complement of (a), (b), (c), (d), (e), (f), or (g).

2. Isolated nucleic acid comprising:

(a) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4);

(b) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking its associatedsignal peptide;

(c) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), withits associated signal peptide;

(d) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4),lacking its associated signal peptide;

(e) the nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQID NO:2);

(f) the full-length coding sequence of the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(g) the full-length coding sequence of the cDNA deposited under any ATCCaccession number shown in Table 7; or

(h) the complement of (a), (b), (c), (d), (e), (f), or (g).

3. Isolated nucleic acid that hybridizes to:

(a) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4);

(b) a nucleotide sequence that encodes the amino acid sequence shown inFIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking its associatedsignal peptide;

(c) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), withits associated signal peptide;

(d) a nucleotide sequence that encodes an extracellular domain of thepolypeptide shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4),lacking its associated signal peptide;

(e) the nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQID NO:2);

(f) the full-length coding sequence of the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(g) the full-length coding sequence of the cDNA deposited under any ATCCaccession number shown in Table 7; or

(h) the complement of (a), (b), (c), (d), (e), (f), or (g).

4. The nucleic acid of claim 3, wherein the hybridization occurs understringent conditions.

5. The nucleic acid of claim 3 which is at least about 5 nucleotides inlength.

6. An expression vector comprising the nucleic acid of claim 1.

7. The expression vector of claim 6, wherein said nucleic acid isoperably linked to control sequences recognized by a host celltransformed with the vector.

8. A host cell comprising the expression vector of claim 7.

9. The host cell of claim 8 which is a CHO cell, an E. coli cell or ayeast cell.

10. A process for producing a polypeptide comprising culturing the hostcell of claim 8 under conditions suitable for expression of saidpolypeptide and recovering said polypeptide from the cell culture.

11. An isolated polypeptide having at least 80% amino acid sequenceidentity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

12. An isolated polypeptide comprising:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

13. A chimeric polypeptide comprising the polypeptide of claim 11 fusedto a heterologous polypeptide.

14. The chimeric polypeptide of claim 13, wherein said heterologouspolypeptide is an epitope tag sequence or an Fc region of animmunoglobulin.

15. An isolated antibody which binds to a polypeptide having at least80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

16. The antibody of claim 15 which binds to a polypeptide comprising:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

17. The antibody of claim 15 which is a monoclonal antibody.

18. The antibody of claim 15 which is an antibody fragment.

19. The antibody of claim 15 which is a chimeric or a humanizedantibody.

20. The antibody of claim 15 which is conjugated to a growth inhibitoryagent.

21. The antibody of claim 15 which is conjugated to a cytotoxic agent.

22. The antibody of claim 21, wherein the cytotoxic agent is selectedfrom the group consisting of toxins, antibiotics, radioactive isotopesand nucleolytic enzymes.

23. The antibody of claim 21, wherein the cytotoxic agent is a toxin.

24. The antibody of claim 23, wherein the toxin is selected from thegroup consisting of maytansinoid and calicheamicin.

25. The antibody of claim 23, wherein the toxin is a maytansinoid.

26. The antibody of claim 15 which is produced in bacteria.

27. The antibody of claim 15 which is produced in CHO cells.

28. The antibody of claim 15 which induces death of a cell to which itbinds.

29. The antibody of claim 15 which is detectably labeled.

30. An isolated nucleic acid comprising a nucleotide sequence thatencodes the antibody of claim 15.

31. An expression vector comprising the nucleic acid of claim 30operably linked to control sequences recognized by a host celltransformed with the vector.

32. A host cell comprising the expression vector of claim 31.

33. The host cell of claim 32 which is a CHO cell, an E. coli cell or ayeast cell.

34. A process for producing an antibody comprising culturing the hostcell of claim 32 under conditions suitable for expression of saidantibody and recovering said antibody from the cell culture.

35. An isolated oligopeptide which binds to a polypeptide having atleast 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

36. The oligopeptide of claim 35 which binds to a polypeptidecomprising:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

37. The oligopeptide of claim 35 which is conjugated to a growthinhibitory agent.

38. The oligopeptide of claim 35 which is conjugated to a cytotoxicagent.

39. The oligopeptide of claim 38, wherein the cytotoxic agent isselected from the group consisting of toxins, antibiotics, radioactiveisotopes and nucleolytic enzymes.

40. The oligopeptide of claim 38, wherein the cytotoxic agent is atoxin.

41. The oligopeptide of claim 40, wherein the toxin is selected from thegroup consisting of maytansinoid and calicheamicin.

42. The oligopeptide of claim 40, wherein the toxin is a maytansinoid.

43. The oligopeptide of claim 35 which induces death of a cell to whichit binds.

44. The oligopeptide of claim 35 which is detectably labeled.

45. A TAT binding organic molecule which binds to a polypeptide havingat least 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

46. The organic molecule of claim 45 which binds to a polypeptidecomprising:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4);

(b) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4), lacking its associated signal peptide;

(c) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), with itsassociated signal peptide;

(d) an amino acid sequence of an extracellular domain of the polypeptideshown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQ ID NO:4), lacking itsassociated signal peptide;

(e) an amino acid sequence encoded by the nucleotide sequence shown inFIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ ID NO:2);

(f) an amino acid sequence encoded by the full-length coding sequence ofthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2); or

(g) an amino acid sequence encoded by the full-length coding sequence ofthe cDNA deposited under any ATCC accession number shown in Table 7.

47. The organic molecule of claim 45 which is conjugated to a growthinhibitory agent.

48. The organic molecule of claim 45 which is conjugated to a cytotoxicagent.

49. The organic molecule of claim 48, wherein the cytotoxic agent isselected from the group consisting of toxins, antibiotics, radioactiveisotopes and nucleolytic enzymes.

50. The organic molecule of claim 48, wherein the cytotoxic agent is atoxin.

51. The organic molecule of claim 50, wherein the toxin is selected fromthe group consisting of maytansinoid and calicheamicin.

52. The organic molecule of claim 50, wherein the toxin is amaytansinoid.

53. The organic molecule of claim 45 which induces death of a cell towhich it binds.

54. The organic molecule of claim 45 which is detectably labeled.

55. A composition of matter comprising:

(a) the polypeptide of claim 11;

(b) the chimeric polypeptide of claim 13;

(c) the antibody of claim 15,

(d) the oligopeptide of claim 35; or

(e) the TAT binding organic molecule of claim 45, in combination with acarrier.

56. The composition of matter of claim 55, wherein said carrier is apharmaceutically acceptable carrier.

57. An article of manufacture:

(a) a container; and

(b) the composition of matter of claim 55 contained within saidcontainer.

58. The article of manufacture of claim 57 further comprising a labelaffixed to said container, or a package insert included with saidcontainer, referring to the use of said composition of matter for thetherapeutic treatment of or the diagnostic detection of a cancer.

59. A method of killing a cancer cell that expresses apolypeptide havingat least 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2), said method comprising contacting said cancer cell with anantibody, oligopeptide or organic molecule that binds to saidpolypeptide on said cancer cell, thereby killing said cancer cell.

60. The method of claim 59, wherein said antibody is a monoclonalantibody.

61. The method of claim 59, wherein said antibody is an antibodyfragment.

62. The method of claim 59, wherein said antibody is a chimeric or ahumanized antibody.

63. The method of claim 59, wherein said antibody, oligopeptide ororganic molecule is conjugated to a growth inhibitory agent.

64. The method of claim 59, wherein said antibody, oligopeptide ororganic molecule is conjugated to a cytotoxic agent.

65. The method of claim 64, wherein said cytotoxic agent is selectedfrom the group consisting of toxins, antibiotics, radioactive isotopesand nucleolytic enzymes.

66. The method of claim 64, wherein the cytotoxic agent is a toxin.

67. The method of claim 66, wherein the toxin is selected from the groupconsisting of maytansinoid and calicheamicin.

68. The method of claim 66, wherein the toxin is a maytansinoid.

69. The method of claim 59, wherein said antibody is produced inbacteria.

70. The method of claim 59, wherein said antibody is produced in CHOcells.

71. The method of claim 59, wherein said cancer cell is further exposedto radiation treatment or a chemotherapeutic agent.

72. The method of claim 59, wherein said cancer cell is selected fromthe group consisting of a breast cancer cell, a colorectal cancer cell,a lung cancer cell, an ovarian cancer cell, a central nervous systemcancer cell, a liver cancer cell, a bladder cancer cell, a pancreaticcancer cell, a cervical cancer cell, a melanoma cell and a leukemiacell.

73. The method of claim 59, wherein said cancer cell overexpresses saidpolypeptide as compared to a normal cell of the same tissue origin.

74. A method of therapeutically treating a mammal having a tumorcomprising cells that express a polypeptide having at least 80% aminoacid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2), said method comprising administering to said mammal atherapeutically effective amount of an antibody, oligopeptide or organicmolecule that binds to said polypeptide, thereby effectively treatingsaid mammal.

75. The method of claim 74, wherein said antibody is a monoclonalantibody.

76. The method of claim 74, wherein said antibody is an antibodyfragment.

77. The method of claim 74, wherein said antibody is a chimeric or ahumanized antibody.

78. The method of claim 74, wherein said antibody, oligopeptide ororganic molecule is conjugated to a growth inhibitory agent.

79. The method of claim 74, wherein said antibody, oligopeptide ororganic molecule is conjugated to a cytotoxic agent.

80. The method of claim 79, wherein said cytotoxic agent is selectedfrom the group consisting of toxins, antibiotics, radioactive isotopesand nucleolytic enzymes.

81. The method of claim 79, wherein the cytotoxic agent is a toxin.

82. The method of claim 81, wherein the toxin is selected from the groupconsisting of maytansinoid and calicheamicin.

83. The method of claim 81, wherein the toxin is a maytansinoid.

84. The method of claim 74, wherein said antibody is produced inbacteria.

85. The method of claim 74, wherein said antibody is produced in CHOcells.

86. The method of claim 74, wherein said tumor is further exposed toradiation treatment or a chemotherapeutic agent.

87. The method of claim 74, wherein said tumor is a breast tumor, acolorectal tumor, a lung tumor, an ovarian tumor, a central nervoussystem tumor, a liver tumor, a bladder tumor, a pancreatic tumor, or acervical tumor.

88. A method of determining the presence of a polypeptide in a samplesuspected of containing said polypeptide, wherein said polypeptide hasat least 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2), said method comprising exposing said sample to an antibody,oligopeptide or organic molecule that binds to said polypeptide anddetermining binding of said antibody, oligopeptide or organic moleculeto said polypeptide in said sample.

89. The method of claim 88, wherein said sample comprises a cellsuspected of expressing said polypeptide.

90. The method of claim 89, wherein said cell is a cancer cell.

91. The method of claim 88, wherein said antibody, oligopeptide ororganic molecule is detectably labeled.

92. A method of diagnosing the presence of a tumor in a mammal, saidmethod comprising detecting the level of expression of a gene encoding apolypeptide having at least 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2), in a test sample of tissue cells obtained from said mammal and ina control sample of known normal cells of the same tissue origin,wherein a higher level of expression of said polypeptide in the testsample, as compared to the control sample, is indicative of the presenceof tumor in the mammal from which the test sample was obtained.

93. The method of claim 92, wherein the step detecting the level ofexpression of a gene encoding said polypeptide comprises employing anoligonucleotide in an in situ hybridization or RT-PCR analysis.

94. The method of claim 92, wherein the step detecting the level ofexpression of a gene encoding said polypeptide comprises employing anantibody in an immunohistochemistry analysis.

95. A method of diagnosing the presence of a tumor in a mammal, saidmethod comprising contacting a test sample of tissue cells obtained fromsaid mammal with an antibody, oligopeptide or organic molecule thatbinds to a polypeptide having at least 80% amino acid sequence identityto:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO: 1) or FIG. 2 (SEQ IDNO:2), and detecting the formation of a complex between said antibody,oligopeptide or organic molecule and said polypeptide in the testsample, wherein the formation of a complex is indicative of the presenceof a tumor in said mammal.

96. The method of claim 95, wherein said antibody, oligopeptide ororganic molecule is detectably labeled.

97. The method of claim 95, wherein said test sample of tissue cells isobtained from an individual suspected of having a cancerous tumor.

98. A method for treating or preventing a cell proliferative disorderassociated with increased expression or activity of a polypeptide havingat least 80% amino acid sequence identity to:

(a) the amino acid sequence shown in FIG. 3 (SEQ ID NO:3) or FIG. 4 (SEQID NO:4); or

(b) an amino acid sequence encoded by a nucleotide sequence comprisingthe nucleotide sequence shown in FIG. 1 (SEQ ID NO:1) or FIG. 2 (SEQ IDNO:2), said method comprising administering to a subject in need of suchtreatment an effective amount of an antagonist of a TAT polypeptide.Preferably, the cell proliferative disorder is cancer and the antagonistof said polypeptide.

99. The method of claim 98, wherein said antagonist is an anti-TATpolypeptide antibody, TAT binding oligopeptide, TAT binding organicmolecule or antisense oligonucleotide.

Further embodiments of the present invention will be evident to theskilled artisan upon a reading of the present specification.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a nucleotide sequence (SEQ ID NO: 1) of a TAT291 cDNA,wherein SEQ ID NO:1 is a clone designated herein as “DNA45234-1277”.

FIG. 2 shows a nucleotide sequence (SEQ ID NO:2) of a TAT292 cDNA,wherein SEQ ID NO:2 is a clone designated herein as “DNA37151-1193”.

FIG. 3 shows the amino acid sequence (SEQ ID NO:3) derived from thecoding sequence of SEQ ID NO: 1 shown in FIG. 1.

FIG. 4 shows the amino acid sequence (SEQ ID NO:4) derived from thecoding sequence of SEQ ID NO:2 shown in FIG. 2.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS I. Definitions

The terms “TAT polypeptide” and “TAT” as used herein and whenimmediately followed by a numerical designation, refer to variouspolypeptides, wherein the complete designation (i.e., TAT/number) refersto specific polypeptide sequences as described herein. The terms“TAT/number polypeptide” and “TAT/number” wherein the term “number” isprovided as an actual numerical designation as used herein encompassnative sequence polypeptides, polypeptide variants and fragments ofnative sequence polypeptides and polypeptide variants (which are furtherdefined herein). The TAT polypeptides described herein may be isolatedfrom a variety of sources, such as from human tissue types or fromanother source, or prepared by recombinant or synthetic methods. Theterm “TAT polypeptide” refers to each individual TAT/number polypeptidedisclosed herein. All disclosures in this specification which refer tothe “TAT polypeptide” refer to each of the polypeptides individually aswell as jointly. For example, descriptions of the preparation of,purification of, derivation of, formation of antibodies to or against,formation of TAT binding oligopeptides to or against, formation of TATbinding organic molecules to or against, administration of, compositionscontaining, treatment of a disease with, etc., pertain to eachpolypeptide of the invention individually. The term “TAT polypeptide”also includes variants of the TAT/number polypeptides disclosed herein.

A “native sequence TAT polypeptide” comprises a polypeptide having thesame amino acid sequence as the corresponding TAT polypeptide derivedfrom nature. Such native sequence TAT polypeptides can be isolated fromnature or can be produced by recombinant or synthetic means. The term“native sequence TAT polypeptide” specifically encompassesnaturally-occurring truncated or secreted forms of the specific TATpolypeptide (e.g., an extracellular domain sequence),naturally-occurring variant forms (e.g., alternatively spliced forms)and naturally-occurring allelic variants of the polypeptide. In certainembodiments of the invention, the native sequence TAT polypeptidesdisclosed herein are mature or full-length native sequence polypeptidescomprising the full-length amino acids sequences shown in theaccompanying figures. Start and stop codons (if indicated) are shown inbold font and underlined in the figures. Nucleic acid residues indicatedas “N” in the accompanying figures are any nucleic acid residue.However, while the TAT polypeptides disclosed in the accompanyingfigures are shown to begin with methionine residues designated herein asamino acid position 1 in the figures, it is conceivable and possiblethat other methionine residues located either upstream or downstreamfrom the amino acid position 1 in the figures may be employed as thestarting amino acid residue for the TAT polypeptides.

The TAT polypeptide “extracellular domain” or “ECD” refers to a form ofthe TAT polypeptide which is essentially free of the transmembrane andcytoplasmic domains. Ordinarily, a TAT polypeptide ECD will have lessthan 1% of such transmembrane and/or cytoplasmic domains and preferably,will have less than 0.5% of such domains. It will be understood that anytransmembrane domains identified for the TAT polypeptides of the presentinvention are identified pursuant to criteria routinely employed in theart for identifying that type of hydrophobic domain. The exactboundaries of a transmembrane domain may vary but most likely by no morethan about 5 amino acids at either end of the domain as initiallyidentified herein. Optionally, therefore, an extracellular domain of aTAT polypeptide may contain from about 5 or fewer amino acids on eitherside of the transmembrane domain/extracellular domain boundary asidentified in the Examples or specification and such polypeptides, withor without the associated signal peptide, and nucleic acid encodingthem, are contemplated by the present invention.

The approximate location of the “signal peptides” of the various TATpolypeptides disclosed herein may be shown in the present specificationand/or the accompanying figures. It is noted, however, that theC-terminal boundary of a signal peptide may vary, but most likely by nomore than about 5 amino acids on either side of the signal peptideC-terminal boundary as initially identified herein, wherein theC-terminal boundary of the signal peptide may be identified pursuant tocriteria routinely employed in the art for identifying that type ofamino acid sequence element (e.g., Nielsen et al., Prot. Eng. 10:1-6(1997) and von Heinje et al., Nucl. Acids. Res. 14:4683-4690 (1986)).Moreover, it is also recognized that, in some cases, cleavage of asignal sequence from a secreted polypeptide is not entirely uniform,resulting in more than one secreted species. These mature polypeptides,where the signal peptide is cleaved within no more than about 5 aminoacids on either side of the C-terminal boundary of the signal peptide asidentified herein, and the polynucleotides encoding them, arecontemplated by the present invention.

“TAT polypeptide variant” means a TAT polypeptide, preferably an activeTAT polypeptide, as defined herein having at least about 80% amino acidsequence identity with a full-length native sequence TAT polypeptidesequence as disclosed herein, a TAT polypeptide sequence lacking thesignal peptide as disclosed herein, an extracellular domain of a TATpolypeptide, with or without the signal peptide, as disclosed herein orany other fragment of a full-length TAT polypeptide sequence asdisclosed herein (such as those encoded by a nucleic acid thatrepresents only a portion of the complete coding sequence for afull-length TAT polypeptide). Such TAT polypeptide variants include, forinstance, TAT polypeptides wherein one or more amino acid residues areadded, or deleted, at the N- or C-terminus of the full-length nativeamino acid sequence. Ordinarily, a TAT polypeptide variant will have atleast about 80% amino acid sequence identity, alternatively at leastabout 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% amino acid sequence identity, to afull-length native sequence TAT polypeptide sequence as disclosedherein, a TAT polypeptide sequence lacking the signal peptide asdisclosed herein, an extracellular domain of a TAT polypeptide, with orwithout the signal peptide, as disclosed herein or any otherspecifically defined fragment of a full-length TAT polypeptide sequenceas disclosed herein. Ordinarily, TAT variant polypeptides are at leastabout 10 amino acids in length, alternatively at least about 20, 30, 40,50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190,200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330,340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460, 470,480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600 aminoacids in length, or more. Optionally, TAT variant polypeptides will haveno more than one conservative amino acid substitution as compared to thenative TAT polypeptide sequence, alternatively no more than 2, 3, 4, 5,6, 7, 8, 9, or 10 conservative amino acid substitution as compared tothe native TAT polypeptide sequence.

“Percent (%) amino acid sequence identity” with respect to the TATpolypeptide sequences identified herein is defined as the percentage ofamino acid residues in a candidate sequence that are identical with theamino acid residues in the specific TAT polypeptide sequence, afteraligning the sequences and introducing gaps, if necessary, to achievethe maximum percent sequence identity, and not considering anyconservative substitutions as part of the sequence identity. Alignmentfor purposes of determining percent amino acid sequence identity can beachieved in various ways that are within the skill in the art, forinstance, using publicly available computer software such as BLAST,BLAST-2, ALIGN or Megalign (DNASTAR) software. Those skilled in the artcan determine appropriate parameters for measuring alignment, includingany algorithms needed to achieve maximal alignment over the full lengthof the sequences being compared. For purposes herein, however, % aminoacid sequence identity values are generated using the sequencecomparison computer program ALIGN-2, wherein the complete source codefor the ALIGN-2 program is provided in Table 1 below. The ALIGN-2sequence comparison computer program was authored by Genentech, Inc. andthe source code shown in Table 1 below has been filed with userdocumentation in the U.S. Copyright Office, Washington D.C., 20559,where it is registered under U.S. Copyright Registration No. TXU510087.The ALIGN-2 program is publicly available through Genentech, Inc., SouthSan Francisco, Calif. or may be compiled from the source code providedin Table 1 below. The ALIGN-2 program should be compiled for use on aUNIX operating system, preferably digital UNIX V4.0D. All sequencecomparison parameters are set by the ALIGN-2 program and do not vary.

In situations where ALIGN-2 is employed for amino acid sequencecomparisons, the % amino acid sequence identity of a given amino acidsequence A to, with, or against a given amino acid sequence B (which canalternatively be phrased as a given amino acid sequence A that has orcomprises a certain % amino acid sequence identity to, with, or againsta given amino acid sequence B) is calculated as follows:

100 times the fraction X/Y

where X is the number of amino acid residues scored as identical matchesby the sequence alignment program ALIGN-2 in that program's alignment ofA and B, and where Y is the total number of amino acid residues in B. Itwill be appreciated that where the length of amino acid sequence A isnot equal to the length of amino acid sequence B, the % amino acidsequence identity of A to B will not equal the % amino acid sequenceidentity of B to A. As examples of % amino acid sequence identitycalculations using this method, Tables 2 and 3 demonstrate how tocalculate the % amino acid sequence identity of the amino acid sequencedesignated “Comparison Protein” to the amino acid sequence designated“TAT”, wherein “TAT” represents the amino acid sequence of ahypothetical TAT polypeptide of interest, “Comparison Protein”represents the amino acid sequence of a polypeptide against which the“TAT” polypeptide of interest is being compared, and “X, “Y” and “Z”each represent different hypothetical amino acid residues. Unlessspecifically stated otherwise, all % amino acid sequence identity valuesused herein are obtained as described in the immediately precedingparagraph using the ALIGN-2 computer program.

“TAT variant polynucleotide” or “TAT variant nucleic acid sequence”means a nucleic acid molecule which encodes a TAT polypeptide,preferably an active TAT polypeptide, as defined herein and which has atleast about 80% nucleic acid sequence identity with a nucleotide acidsequence encoding a full-length native sequence TAT polypeptide sequenceas disclosed herein, a full-length native sequence TAT polypeptidesequence lacking the signal peptide as disclosed herein, anextracellular domain of a TAT polypeptide, with or without the signalpeptide, as disclosed herein or any other fragment of a full-length TATpolypeptide sequence as disclosed herein (such as those encoded by anucleic acid that represents only a portion of the complete codingsequence for a full-length TAT polypeptide). Ordinarily, a TAT variantpolynucleotide will have at least about 80% nucleic acid sequenceidentity, alternatively at least about 81%, 82%, 83%, 84%, 85%, 86%,87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%nucleic acid sequence identity with a nucleic acid sequence encoding afull-length native sequence TAT polypeptide sequence as disclosedherein, a full-length native sequence TAT polypeptide sequence lackingthe signal peptide as disclosed herein, an extracellular domain of a TATpolypeptide, with or without the signal sequence, as disclosed herein orany other fragment of a full-length TAT polypeptide sequence asdisclosed herein. Variants do not encompass the native nucleotidesequence.

Ordinarily, TAT variant polynucleotides are at least about 5 nucleotidesin length, alternatively at least about 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40,45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110, 115, 120,125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180, 185, 190,195, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320,330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 450, 460,470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600,610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740,750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880,890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000nucleotides in length, wherein in this context the term “about” meansthe referenced nucleotide sequence length plus or minus 10% of thatreferenced length.

“Percent (%) nucleic acid sequence identity” with respect toTAT-encoding nucleic acid sequences identified herein is defined as thepercentage of nucleotides in a candidate sequence that are identicalwith the nucleotides in the TAT nucleic acid sequence of interest, afteraligning the sequences and introducing gaps, if necessary, to achievethe maximum percent sequence identity. Alignment for purposes ofdetermining percent nucleic acid sequence identity can be achieved invarious ways that are within the skill in the art, for instance, usingpublicly available computer software such as BLAST, BLAST-2, ALIGN orMegalign (DNASTAR) software. For purposes herein, however, % nucleicacid sequence identity values are generated using the sequencecomparison computer program ALIGN-2, wherein the complete source codefor the ALIGN-2 program is provided in Table 1 below. The ALIGN-2sequence comparison computer program was authored by Genentech, Inc. andthe source code shown in Table 1 below has been filed with userdocumentation in the U.S. Copyright Office, Washington D.C., 20559,where it is registered under U.S. Copyright Registration No. TXU510087.The ALIGN-2 program is publicly available through Genentech, Inc., SouthSan Francisco, Calif. or may be compiled from the source code providedin Table 1 below. The ALIGN-2 program should be compiled for use on aUNIX operating system, preferably digital UNIX V4.0D. All sequencecomparison parameters are set by the ALIGN-2 program and do not vary.

In situations where ALIGN-2 is employed for nucleic acid sequencecomparisons, the % nucleic acid sequence identity of a given nucleicacid sequence C to, with, or against a given nucleic acid sequence D(which can alternatively be phrased as a given nucleic acid sequence Cthat has or comprises a certain % nucleic acid sequence identity to,with, or against a given nucleic acid sequence D) is calculated asfollows:

100 times the fraction W/Z

where W is the number of nucleotides scored as identical matches by thesequence alignment program ALIGN-2 in that program's alignment of C andD, and where Z is the total number of nucleotides in D. It will beappreciated that where the length of nucleic acid sequence C is notequal to the length of nucleic acid sequence D, the % nucleic acidsequence identity of C to D will not equal the % nucleic acid sequenceidentity of D to C. As examples of % nucleic acid sequence identitycalculations, Tables 4 and 5, demonstrate how to calculate the % nucleicacid sequence identity of the nucleic acid sequence designated“Comparison DNA” to the nucleic acid sequence designated “TAT-DNA”,wherein “TAT-DNA” represents a hypothetical TAT-encoding nucleic acidsequence of interest, “Comparison DNA” represents the nucleotidesequence of a nucleic acid molecule against which the “TAT-DNA” nucleicacid molecule of interest is being compared, and “N”, “L” and “V” eachrepresent different hypothetical nucleotides. Unless specifically statedotherwise, all % nucleic acid sequence identity values used herein areobtained as described in the immediately preceding paragraph using theALIGN-2 computer program.

In other embodiments, TAT variant polynucleotides are nucleic acidmolecules that encode a TAT polypeptide and which are capable ofhybridizing, preferably under stringent hybridization and washconditions, to nucleotide sequences encoding a full-length TATpolypeptide as disclosed herein. TAT variant polypeptides may be thosethat are encoded by a TAT variant polynucleotide.

“Isolated,” when used to describe the various TAT polypeptides disclosedherein, means polypeptide that has been identified and separated and/orrecovered from a component of its natural environment. Contaminantcomponents of its natural environment are materials that would typicallyinterfere with diagnostic or therapeutic uses for the polypeptide, andmay include enzymes, hormones, and other proteinaceous ornon-proteinaceous solutes. In preferred embodiments, the polypeptidewill be purified (1) to a degree sufficient to obtain at least 15residues of N-terminal or internal amino acid sequence by use of aspinning cup sequenator, or (2) to homogeneity by SDS-PAGE undernon-reducing or reducing conditions using Coomassie blue or, preferably,silver stain. Isolated polypeptide includes polypeptide in situ withinrecombinant cells, since at least one component of the TAT polypeptidenatural environment will not be present. Ordinarily, however, isolatedpolypeptide will be prepared by at least one purification step.

An “isolated” TAT polypeptide-encoding nucleic acid or otherpolypeptide-encoding nucleic acid is a nucleic acid molecule that isidentified and separated from at least one contaminant nucleic acidmolecule with which it is ordinarily associated in the natural source ofthe polypeptide-encoding nucleic acid. An isolated polypeptide-encodingnucleic acid molecule is other than in the form or setting in which itis found in nature. Isolated polypeptide-encoding nucleic acid moleculestherefore are distinguished from the specific polypeptide-encodingnucleic acid molecule as it exists in natural cells. However, anisolated polypeptide-encoding nucleic acid molecule includespolypeptide-encoding nucleic acid molecules contained in cells thatordinarily express the polypeptide where, for example, the nucleic acidmolecule is in a chromosomal location different from that of naturalcells.

The term “control sequences” refers to DNA sequences necessary for theexpression of an operably linked coding sequence in a particular hostorganism. The control sequences that are suitable for prokaryotes, forexample, include a promoter, optionally an operator sequence, and aribosome binding site. Eukaryotic cells are known to utilize promoters,polyadenylation signals, and enhancers.

Nucleic acid is “operably linked” when it is placed into a functionalrelationship with another nucleic acid sequence. For example, DNA for apresequence or secretory leader is operably linked to DNA for apolypeptide if it is expressed as a preprotein that participates in thesecretion of the polypeptide; a promoter or enhancer is operably linkedto a coding sequence if it affects the transcription of the sequence; ora ribosome binding site is operably linked to a coding sequence if it ispositioned so as to facilitate translation. Generally, “operably linked”means that the DNA sequences being linked are contiguous, and, in thecase of a secretory leader, contiguous and in reading phase. However,enhancers do not have to be contiguous. Linking is accomplished byligation at convenient restriction sites. If such sites do not exist,the synthetic oligonucleotide adaptors or linkers are used in accordancewith conventional practice.

“Stringency” of hybridization reactions is readily determinable by oneof ordinary skill in the art, and generally is an empirical calculationdependent upon probe length, washing temperature, and saltconcentration. In general, longer probes require higher temperatures forproper annealing, while shorter probes need lower temperatures.Hybridization generally depends on the ability of denatured DNA toreanneal when complementary strands are present in an environment belowtheir melting temperature. The higher the degree of desired homologybetween the probe and hybridizable sequence, the higher the relativetemperature which can be used. As a result, it follows that higherrelative temperatures would tend to make the reaction conditions morestringent, while lower temperatures less so. For additional details andexplanation of stringency of hybridization reactions, see Ausubel etal., Current Protocols in Molecular Biology, Wiley IntersciencePublishers, (1995).

“Stringent conditions” or “high stringency conditions”, as definedherein, may be identified by those that: (1) employ low ionic strengthand high temperature for washing, for example 0.015 M sodiumchloride/0.0015 M sodium citrate/0.1% sodium dodecyl sulfate at 50° C.;(2) employ during hybridization a denaturing agent, such as formamide,for example, 50% (v/v) formamide with 0.1% bovine serum albumin/0.1%Ficoll/0.1% polyvinylpyrrolidone/50 mM sodium phosphate buffer at pH 6.5with 750 mM sodium chloride, 75 mM sodium citrate at 42° C.; or (3)employ 50% formamide, 5×SSC (0.75 M NaCl, 0.075 M sodium citrate), 50 mMsodium phosphate (pH 6.8), 0.1% sodium pyrophosphate, 5×Denhardt'ssolution, sonicated salmon sperm DNA (50 μg/ml), 0.1% SDS, and 10%dextran sulfate at 42° C., with washes at 42° C. in 0.2×SSC (sodiumchloride/sodium citrate) and 50% formamide at 55° C., followed by ahigh-stringency wash consisting of 0.1×SSC containing EDTA at 55° C.

“Moderately stringent conditions” may be identified as described bySambrook et al., Molecular Cloning: A Laboratory Manual, New York: ColdSpring Harbor Press, 1989, and include the use of washing solution andhybridization conditions (e.g., temperature, ionic strength and % SDS)less stringent that those described above. An example of moderatelystringent conditions is overnight incubation at 37° C. in a solutioncomprising: 20% formamide, 5×SSC (150 mM NaCl, 15 mM trisodium citrate),50 mM sodium phosphate (pH 7.6), 5×Denhardt's solution, 10% dextransulfate, and 20 mg/ml denatured sheared salmon sperm DNA, followed bywashing the filters in 1×SSC at about 37-50° C. The skilled artisan willrecognize how to adjust the temperature, ionic strength, etc. asnecessary to accommodate factors such as probe length and the like.

The term “epitope tagged” when used herein refers to a chimericpolypeptide comprising a TAT polypeptide or anti-TAT antibody fused to a“tag polypeptide”. The tag polypeptide has enough residues to provide anepitope against which an antibody can be made, yet is short enough suchthat it does not interfere with activity of the polypeptide to which itis fused. The tag polypeptide preferably also is fairly unique so thatthe antibody does not substantially cross-react with other epitopes.Suitable tag polypeptides generally have at least six amino acidresidues and usually between about 8 and 50 amino acid residues(preferably, between about 10 and 20 amino acid residues).

“Active” or “activity” for the purposes herein refers to form(s) of aTAT polypeptide which retain a biological and/or an immunologicalactivity of native or naturally-occurring TAT, wherein “biological”activity refers to a biological function (either inhibitory orstimulatory) caused by a native or naturally-occurring TAT other thanthe ability to induce the production of an antibody against an antigenicepitope possessed by a native or naturally-occurring TAT and an“immunological” activity refers to the ability to induce the productionof an antibody against an antigenic epitope possessed by a native ornaturally-occurring TAT.

The term “antagonist” is used in the broadest sense, and includes anymolecule that partially or fully blocks, inhibits, or neutralizes abiological activity of a native TAT polypeptide disclosed herein. In asimilar manner, the term “agonist” is used in the broadest sense andincludes any molecule that mimics a biological activity of a native TATpolypeptide disclosed herein. Suitable agonist or antagonist moleculesspecifically include agonist or antagonist antibodies or antibodyfragments, fragments or amino acid sequence variants of native TATpolypeptides, peptides, antisense oligonucleotides, small organicmolecules, etc. Methods for identifying agonists or antagonists of a TATpolypeptide may comprise contacting a TAT polypeptide with a candidateagonist or antagonist molecule and measuring a detectable change in oneor more biological activities normally associated with the TATpolypeptide.

“Treating” or “treatment” or “alleviation” refers to both therapeutictreatment and prophylactic or preventative measures, wherein the objectis to prevent or slow down (lessen) the targeted pathologic condition ordisorder. Those in need of treatment include those already with thedisorder as well as those prone to have the disorder or those in whomthe disorder is to be prevented. A subject or mammal is successfully“treated” for a TAT polypeptide-expressing cancer if, after receiving atherapeutic amount of an anti-TAT antibody, TAT binding oligopeptide orTAT binding organic molecule according to the methods of the presentinvention, the patient shows observable and/or measurable reduction inor absence of one or more of the following: reduction in the number ofcancer cells or absence of the cancer cells; reduction in the tumorsize; inhibition (i.e., slow to some extent and preferably stop) ofcancer cell infiltration into peripheral organs including the spread ofcancer into soft tissue and bone; inhibition (i.e., slow to some extentand preferably stop) of tumor metastasis; inhibition, to some extent, oftumor growth; and/or relief to some extent, one or more of the symptomsassociated with the specific cancer; reduced morbidity and mortality,and improvement in quality of life issues. To the extent the anti-TATantibody or TAT binding oligopeptide may prevent growth and/or killexisting cancer cells, it may be cytostatic and/or cytotoxic. Reductionof these signs or symptoms may also be felt by the patient.

The above parameters for assessing successful treatment and improvementin the disease are readily measurable by routine procedures familiar toa physician. For cancer therapy, efficacy can be measured, for example,by assessing the time to disease progression (TTP) and/or determiningthe response rate (RR). Metastasis can be determined by staging testsand by bone scan and tests for calcium level and other enzymes todetermine spread to the bone. CT scans can also be done to look forspread to the pelvis and lymph nodes in the area. Chest X-rays andmeasurement of liver enzyme levels by known methods are used to look formetastasis to the lungs and liver, respectively. Other routine methodsfor monitoring the disease include transrectal ultrasonography (TRUS)and transrectal needle biopsy (TRNB).

For bladder cancer, which is a more localized cancer, methods todetermine progress of disease include urinary cytologic evaluation bycystoscopy, monitoring for presence of blood in the urine, visualizationof the urothelial tract by sonography or an intravenous pyelogram,computed tomography (CT) and magnetic resonance imaging (MRI). Thepresence of distant metastases can be assessed by CT of the abdomen,chest x-rays, or radionuclide imaging of the skeleton.

“Chronic” administration refers to administration of the agent(s) in acontinuous mode as opposed to an acute mode, so as to maintain theinitial therapeutic effect (activity) for an extended period of time.“Intermittent” administration is treatment that is not consecutivelydone without interruption, but rather is cyclic in nature.

“Mammal” for purposes of the treatment of, alleviating the symptoms ofor diagnosis of a cancer refers to any animal classified as a mammal,including humans, domestic and farm animals, and zoo, sports, or petanimals, such as dogs, cats, cattle, horses, sheep, pigs, goats,rabbits, etc. Preferably, the mammal is human.

Administration “in combination with” one or more further therapeuticagents includes simultaneous (concurrent) and consecutive administrationin any order.

“Carriers” as used herein include pharmaceutically acceptable carriers,excipients, or stabilizers which are nontoxic to the cell or mammalbeing exposed thereto at the dosages and concentrations employed. Oftenthe physiologically acceptable carrier is an aqueous pH bufferedsolution. Examples of physiologically acceptable carriers includebuffers such as phosphate, citrate, and other organic acids;antioxidants including ascorbic acid; low molecular weight (less thanabout 10 residues) polypeptide; proteins, such as serum albumin,gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, arginine or lysine; monosaccharides, disaccharides, andother carbohydrates including glucose, mannose, or dextrins; chelatingagents such as EDTA; sugar alcohols such as mannitol or sorbitol;salt-forming counterions such as sodium; and/or nonionic surfactantssuch as TWEEN®, polyethylene glycol (PEG), and PLURONICS®.

By “solid phase” or “solid support” is meant a non-aqueous matrix towhich an antibody, TAT binding oligopeptide or TAT binding organicmolecule of the present invention can adhere or attach. Examples ofsolid phases encompassed herein include those formed partially orentirely of glass (e.g., controlled pore glass), polysaccharides (e.g.,agarose), polyacrylamides, polystyrene, polyvinyl alcohol and silicones.In certain embodiments, depending on the context, the solid phase cancomprise the well of an assay plate; in others it is a purificationcolumn (e.g., an affinity chromatography column). This term alsoincludes a discontinuous solid phase of discrete particles, such asthose described in U.S. Pat. No. 4,275,149.

A “liposome” is a small vesicle composed of various types of lipids,phospholipids and/or surfactant which is useful for delivery of a drug(such as a TAT polypeptide, an antibody thereto or a TAT bindingoligopeptide) to a mammal. The components of the liposome are commonlyarranged in a bilayer formation, similar to the lipid arrangement ofbiological membranes.

A “small” molecule or “small” organic molecule is defined herein to havea molecular weight below about 500 Daltons.

An “effective amount” of a polypeptide, antibody, TAT bindingoligopeptide, TAT binding organic molecule or an agonist or antagonistthereof as disclosed herein is an amount sufficient to carry out aspecifically stated purpose. An “effective amount” may be determinedempirically and in a routine manner, in relation to the stated purpose.

The term “therapeutically effective amount” refers to an amount of anantibody, polypeptide, TAT binding oligopeptide, TAT binding organicmolecule or other drug effective to “treat” a disease or disorder in asubject or mammal. In the case of cancer, the therapeutically effectiveamount of the drug may reduce the number of cancer cells; reduce thetumor size; inhibit (i.e., slow to some extent and preferably stop)cancer cell infiltration into peripheral organs; inhibit (i.e., slow tosome extent and preferably stop) tumor metastasis; inhibit, to someextent, tumor growth; and/or relieve to some extent one or more of thesymptoms associated with the cancer. See the definition herein of“treating”. To the extent the drug may prevent growth and/or killexisting cancer cells, it may be cytostatic and/or cytotoxic.

A “growth inhibitory amount” of an anti-TAT antibody, TAT polypeptide,TAT binding oligopeptide or TAT binding organic molecule is an amountcapable of inhibiting the growth of a cell, especially tumor, e.g.,cancer cell, either in vitro or in vivo. A “growth inhibitory amount” ofan anti-TAT antibody, TAT polypeptide, TAT binding oligopeptide or TATbinding organic molecule for purposes of inhibiting neoplastic cellgrowth may be determined empirically and in a routine manner.

A “cytotoxic amount” of an anti-TAT antibody, TAT polypeptide, TATbinding oligopeptide or TAT binding organic molecule is an amountcapable of causing the destruction of a cell, especially tumor, e.g.,cancer cell, either in vitro or in vivo. A “cytotoxic amount” of ananti-TAT antibody, TAT polypeptide, TAT binding oligopeptide or TATbinding organic molecule for purposes of inhibiting neoplastic cellgrowth may be determined empirically and in a routine manner.

The term “antibody” is used in the broadest sense and specificallycovers, for example, single anti-TAT monoclonal antibodies (includingagonist, antagonist, and neutralizing antibodies), anti-TAT antibodycompositions with polyepitopic specificity, polyclonal antibodies,single chain anti-TAT antibodies, and fragments of anti-TAT antibodies(see below) as long as they exhibit the desired biological orimmunological activity. The term “immunoglobulin” (Ig) is usedinterchangeable with antibody herein.

An “isolated antibody” is one which has been identified and separatedand/or recovered from a component of its natural environment.Contaminant components of its natural environment are materials whichwould interfere with diagnostic or therapeutic uses for the antibody,and may include enzymes, hormones, and other proteinaceous ornonproteinaceous solutes. In preferred embodiments, the antibody will bepurified (1) to greater than 95% by weight of antibody as determined bythe Lowry method, and most preferably more than 99% by weight, (2) to adegree sufficient to obtain at least 15 residues of N-terminal orinternal amino acid sequence by use of a spinning cup sequenator, or (3)to homogeneity by SDS-PAGE under reducing or nonreducing conditionsusing Coomassie blue or, preferably, silver stain. Isolated antibodyincludes the antibody in situ within recombinant cells since at leastone component of the antibody's natural environment will not be present.Ordinarily, however, isolated antibody will be prepared by at least onepurification step.

The basic 4-chain antibody unit is a heterotetrameric glycoproteincomposed of two identical light (L) chains and two identical heavy (H)chains (an IgM antibody consists of 5 of the basic heterotetramer unitalong with an additional polypeptide called J chain, and thereforecontain 10 antigen binding sites, while secreted IgA antibodies canpolymerize to form polyvalent assemblages comprising 2-5 of the basic4-chain units along with J chain). In the case of IgGs, the 4-chain unitis generally about 150,000 daltons. Each L chain is linked to a H chainby one covalent disulfide bond, while the two H chains are linked toeach other by one or more disulfide bonds depending on the H chainisotype. Each H and L chain also has regularly spaced intrachaindisulfide bridges. Each H chain has at the N-terminus, a variable domain(V_(H)) followed by three constant domains (C_(H)) for each of the α andγ chains and four C_(H) domains for μ and isotypes. Each L chain has atthe N-terminus, a variable domain (V_(L)) followed by a constant domain(C_(L)) at its other end. The V_(L) is aligned with the V_(H) and theC_(L) is aligned with the first constant domain of the heavy chain(C_(H)1). Particular amino acid residues are believed to form aninterface between the light chain and heavy chain variable domains. Thepairing of a V_(H) and V_(L) together forms a single antigen-bindingsite. For the structure and properties of the different classes ofantibodies, see, e.g., Basic and Clinical Immunology, 8th edition,Daniel P. Stites, Abba I. Terr and Tristram G. Parslow (eds.), Appleton& Lange, Norwalk, Conn., 1994, page 71 and Chapter 6.

The L chain from any vertebrate species can be assigned to one of twoclearly distinct types, called kappa and lambda, based on the amino acidsequences of their constant domains. Depending on the amino acidsequence of the constant domain of their heavy chains (C_(H)),immunoglobulins can be assigned to different classes or isotypes. Thereare five classes of immunoglobulins: IgA, IgD, IgE, IgG, and IgM, havingheavy chains designated α, δ, ε, γ, and μ, respectively. The γ and αclasses are further divided into subclasses on the basis of relativelyminor differences in C_(H) sequence and function, e.g., humans expressthe following subclasses: IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2.

The term “variable” refers to the fact that certain segments of thevariable domains differ extensively in sequence among antibodies. The Vdomain mediates antigen binding and define specificity of a particularantibody for its particular antigen. However, the variability is notevenly distributed across the 110-amino acid span of the variabledomains. Instead, the V regions consist of relatively invariantstretches called framework regions (FRs) of 15-30 amino acids separatedby shorter regions of extreme variability called “hypervariable regions”that are each 9-12 amino acids long. The variable domains of nativeheavy and light chains each comprise four FRs, largely adopting aβ-sheet configuration, connected by three hypervariable regions, whichform loops connecting, and in some cases forming part of, the β-sheetstructure. The hypervariable regions in each chain are held together inclose proximity by the FRs and, with the hypervariable regions from theother chain, contribute to the formation of the antigen-binding site ofantibodies (see Kabat et al., Sequences of Proteins of ImmunologicalInterest, 5th Ed. Public Health Service, National Institutes of Health,Bethesda, Md. (1991)). The constant domains are not involved directly inbinding an antibody to an antigen, but exhibit various effectorfunctions, such as participation of the antibody in antibody dependentcellular cytotoxicity (ADCC).

The term “hypervariable region” when used herein refers to the aminoacid residues of an antibody which are responsible for antigen-binding.The hypervariable region generally comprises amino acid residues from a“complementarity determining region” or “CDR” (e.g. around aboutresidues 24-34 (L1), 50-56 (L2) and 89-97 (L3) in the V_(L), and aroundabout 1-35 (H1), 50-65 (H2) and 95-102 (H3) in the V_(H); Kabat et al.,Sequences of Proteins of Immunological Interest, 5th Ed. Public HealthService, National Institutes of Health, Bethesda, Md. (1991)) and/orthose residues from a “hypervariable loop” (e.g. residues 26-32 (L1),50-52 (L2) and 91-96 (L3) in the V_(L), and 26-32 (H1), 53-55 (H2) and96-101 (H3) in the V_(H); Chothia and Lesk J. Mol. Biol. 196:901-917(1987)).

The term “monoclonal antibody” as used herein refers to an antibodyobtained from a population of substantially homogeneous antibodies,i.e., the individual antibodies comprising the population are identicalexcept for possible naturally occurring mutations that may be present inminor amounts. Monoclonal antibodies are highly specific, being directedagainst a single antigenic site. Furthermore, in contrast to polyclonalantibody preparations which include different antibodies directedagainst different determinants (epitopes), each monoclonal antibody isdirected against a single determinant on the antigen. In addition totheir specificity, the monoclonal antibodies are advantageous in thatthey may be synthesized uncontaminated by other antibodies. The modifier“monoclonal” is not to be construed as requiring production of theantibody by any particular method. For example, the monoclonalantibodies useful in the present invention may be prepared by thehybridoma methodology first described by Kohler et al., Nature, 256:495(1975), or may be made using recombinant DNA methods in bacterial,eukaryotic animal or plant cells (see, e.g., U.S. Pat. No. 4,816,567).The “monoclonal antibodies” may also be isolated from phage antibodylibraries using the techniques described in Clackson et al., Nature,352:624-628 (1991) and Marks et al., J. Mol. Biol., 222:581-597 (1991),for example.

The monoclonal antibodies herein include “chimeric” antibodies in whicha portion of the heavy and/or light chain is identical with orhomologous to corresponding sequences in antibodies derived from aparticular species or belonging to a particular antibody class orsubclass, while the remainder of the chain(s) is identical with orhomologous to corresponding sequences in antibodies derived from anotherspecies or belonging to another antibody class or subclass, as well asfragments of such antibodies, so long as they exhibit the desiredbiological activity (see U.S. Pat. No. 4,816,567; and Morrison et al.,Proc. Natl. Acad. Sci. USA, 81:6851-6855 (1984)). Chimeric antibodies ofinterest herein include “primatized” antibodies comprising variabledomain antigen-binding sequences derived from a non-human primate (e.g.Old World Monkey, Ape etc), and human constant region sequences.

An “intact” antibody is one which comprises an antigen-binding site aswell as a C_(L) and at least heavy chain constant domains, C_(H)1,C_(H)2 and C_(H)3. The constant domains may be native sequence constantdomains (e.g. human native sequence constant domains) or amino acidsequence variant thereof. Preferably, the intact antibody has one ormore effector functions.

“Antibody fragments” comprise a portion of an intact antibody,preferably the antigen binding or variable region of the intactantibody. Examples of antibody fragments include Fab, Fab′, F(ab′)₂, andFv fragments; diabodies; linear antibodies (see U.S. Pat. No. 5,641,870,Example 2; Zapata et al., Protein Eng. 8(10): 1057-1062 [1995]);single-chain antibody molecules; and multispecific antibodies formedfrom antibody fragments.

Papain digestion of antibodies produces two identical antigen-bindingfragments, called “Fab” fragments, and a residual “Fc” fragment, adesignation reflecting the ability to crystallize readily. The Fabfragment consists of an entire L chain along with the variable regiondomain of the H chain (V_(H)), and the first constant domain of oneheavy chain (C_(H)1). Each Fab fragment is monovalent with respect toantigen binding, i.e., it has a single antigen-binding site. Pepsintreatment of an antibody yields a single large F(ab′)₂ fragment whichroughly corresponds to two disulfide linked Fab fragments havingdivalent antigen-binding activity and is still capable of cross-linkingantigen. Fab′ fragments differ from Fab fragments by having additionalfew residues at the carboxy terminus of the C_(H)1 domain including oneor more cysteines from the antibody hinge region. Fab′-SH is thedesignation herein for Fab′ in which the cysteine residue(s) of theconstant domains bear a free thiol group. F(ab′)₂ antibody fragmentsoriginally were produced as pairs of Fab′ fragments which have hingecysteines between them. Other chemical couplings of antibody fragmentsare also known.

The Fc fragment comprises the carboxy-terminal portions of both H chainsheld together by disulfides. The effector functions of antibodies aredetermined by sequences in the Fc region, which region is also the partrecognized by Fc receptors (FcR) found on certain types of cells.

“Fv” is the minimum antibody fragment which contains a completeantigen-recognition and -binding site. This fragment consists of a dimerof one heavy- and one light-chain variable region domain in tight,non-covalent association. From the folding of these two domains emanatesix hypervariable loops (3 loops each from the H and L chain) thatcontribute the amino acid residues for antigen binding and conferantigen binding specificity to the antibody. However, even a singlevariable domain (or half of an Fv comprising only three CDRs specificfor an antigen) has the ability to recognize and bind antigen, althoughat a lower affinity than the entire binding site.

“Single-chain Fv” also abbreviated as “sFv” or “scFv” are antibodyfragments that comprise the V_(H) and V_(L) antibody domains connectedinto a single polypeptide chain. Preferably, the sFv polypeptide furthercomprises a polypeptide linker between the V_(H) and V_(L) domains whichenables the sFv to form the desired structure for antigen binding. For areview of sFv, see Pluckthun in The Pharmacology of MonoclonalAntibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, NewYork, pp. 269-315 (1994); Borrebaeck 1995, infra.

The term “diabodies” refers to small antibody fragments prepared byconstructing sFv fragments (see preceding paragraph) with short linkers(about 5-10 residues) between the V_(H) and V_(L) domains such thatinter-chain but not intra-chain pairing of the V domains is achieved,resulting in a bivalent fragment, i.e., fragment having twoantigen-binding sites. Bispecific diabodies are heterodimers of two“crossover” sFv fragments in which the V_(H) and V_(L) domains of thetwo antibodies are present on different polypeptide chains. Diabodiesare described more fully in, for example, EP 404,097; WO 93/11161; andHollinger et al., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993).

“Humanized” forms of non-human (e.g., rodent) antibodies are chimericantibodies that contain minimal sequence derived from the non-humanantibody. For the most part, humanized antibodies are humanimmunoglobulins (recipient antibody) in which residues from ahypervariable region of the recipient are replaced by residues from ahypervariable region of a non-human species (donor antibody) such asmouse, rat, rabbit or non-human primate having the desired antibodyspecificity, affinity, and capability. In some instances, frameworkregion (FR) residues of the human immunoglobulin are replaced bycorresponding non-human residues. Furthermore, humanized antibodies maycomprise residues that are not found in the recipient antibody or in thedonor antibody. These modifications are made to further refine antibodyperformance. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the hypervariable loops correspondto those of a non-human immunoglobulin and all or substantially all ofthe FRs are those of a human immunoglobulin sequence. The humanizedantibody optionally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin. For further details, see Jones et al., Nature321:522-525 (1986); Riechmann et al., Nature 332:323-329 (1988); andPresta, Curr. Op. Struct. Biol. 2: 593-596 (1992).

A “species-dependent antibody,” e.g., a mammalian anti-human IgEantibody, is an antibody which has a stronger binding affinity for anantigen from a first mammalian species than it has for a homologue ofthat antigen from a second mammalian species. Normally, thespecies-dependent antibody “bind specifically” to a human antigen (i.e.,has a binding affinity (Kd) value of no more than about 1×10⁻⁷ M,preferably no more than about 1×10⁻⁸ and most preferably no more thanabout 1×10⁻⁹ M) but has a binding affinity for a homologue of theantigen from a second non-human mammalian species which is at leastabout 50 fold, or at least about 500 fold, or at least about 1000 fold,weaker than its binding affinity for the human antigen. Thespecies-dependent antibody can be of any of the various types ofantibodies as defined above, but preferably is a humanized or humanantibody.

A “TAT binding oligopeptide” is an oligopeptide that binds, preferablyspecifically, to a TAT polypeptide as described herein. TAT bindingoligopeptides may be chemically synthesized using known oligopeptidesynthesis methodology or may be prepared and purified using recombinanttechnology. TAT binding oligopeptides are usually at least about 5 aminoacids in length, alternatively at least about 6, 7, 8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84,85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 aminoacids in length or more, wherein such oligopeptides that are capable ofbinding, preferably specifically, to a TAT polypeptide as describedherein. TAT binding oligopeptides may be identified without undueexperimentation using well known techniques. In this regard, it is notedthat techniques for screening oligopeptide libraries for oligopeptidesthat are capable of specifically binding to a polypeptide target arewell known in the art (see, e.g., U.S. Pat. Nos. 5,556,762, 5,750,373,4,708,871, 4,833,092, 5,223,409, 5,403,484, 5,571,689, 5,663,143; PCTPublication Nos. WO 84/03506 and WO84/03564; Geysen et al., Proc. Natl.Acad. Sci. U.S.A., 81:3998-4002 (1984); Geysen et al., Proc. Natl. Acad.Sci. U.S.A., 82:178-182 (1985); Geysen et al., in Synthetic Peptides asAntigens, 130-149 (1986); Geysen et al., J. Immunol. Meth., 102:259-274(1987); Schoofs et al., J. Immunol., 140:611-616 (1988), Cwirla, S. E.et al. (1990) Proc. Natl. Acad. Sci. USA, 87:6378; Lowman, H. B. et al.(1991) Biochemistry, 30:10832; Clackson, T. et al. (1991) Nature, 352:624; Marks, J. D. et al. (1991), J. Mol. Biol., 222:581; Kang, A. S. etal. (1991) Proc. Natl. Acad. Sci. USA, 88:8363, and Smith, G. P. (1991)Current Opin. Biotechnol., 2:668).

A “TAT binding organic molecule” is an organic molecule other than anoligopeptide or antibody as defined herein that binds, preferablyspecifically, to a TAT polypeptide as described herein. TAT bindingorganic molecules may be identified and chemically synthesized usingknown methodology (see, e.g., PCT Publication Nos. WO00/00823 andWO00/39585). TAT binding organic molecules are usually less than about2000 daltons in size, alternatively less than about 1500, 750, 500, 250or 200 daltons in size, wherein such organic molecules that are capableof binding, preferably specifically, to a TAT polypeptide as describedherein may be identified without undue experimentation using well knowntechniques. In this regard, it is noted that techniques for screeningorganic molecule libraries for molecules that are capable of binding toa polypeptide target are well known in the art (see, e.g., PCTPublication Nos. WO00/00823 and WO00/39585).

An antibody, oligopeptide or other organic molecule “which binds” anantigen of interest, e.g. a tumor-associated polypeptide antigen target,is one that binds the antigen with sufficient affinity such that theantibody, oligopeptide or other organic molecule is useful as adiagnostic and/or therapeutic agent in targeting a cell or tissueexpressing the antigen, and does not significantly cross-react withother proteins. In such embodiments, the extent of binding of theantibody, oligopeptide or other organic molecule to a “non-target”protein will be less than about 10% of the binding of the antibody,oligopeptide or other organic molecule to its particular target proteinas determined by fluorescence activated cell sorting (FACS) analysis orradioimmunoprecipitation (RIA). With regard to the binding of anantibody, oligopeptide or other organic molecule to a target molecule,the term “specific binding” or “specifically binds to” or is “specificfor” a particular polypeptide or an epitope on a particular polypeptidetarget means binding that is measurably different from a non-specificinteraction. Specific binding can be measured, for example, bydetermining binding of a molecule compared to binding of a controlmolecule, which generally is a molecule of similar structure that doesnot have binding activity. For example, specific binding can bedetermined by competition with a control molecule that is similar to thetarget, for example, an excess of non-labeled target. In this case,specific binding is indicated if the binding of the labeled target to aprobe is competitively inhibited by excess unlabeled target. The term“specific binding” or “specifically binds to” or is “specific for” aparticular polypeptide or an epitope on a particular polypeptide targetas used herein can be exhibited, for example, by a molecule having a Kdfor the target of at least about 10⁻⁴ M, alternatively at least about10⁻⁵ M, alternatively at least about 10⁻⁶ M, alternatively at leastabout 10⁻⁷ M, alternatively at least about 10⁻⁸ M, alternatively atleast about 10⁻⁹ M, alternatively at least about 10⁻¹⁰ M, alternativelyat least about 10⁻¹¹ M, alternatively at least about 10⁻¹² M, orgreater. In one embodiment, the term “specific binding” refers tobinding where a molecule binds to a particular polypeptide or epitope ona particular polypeptide without substantially binding to any otherpolypeptide or polypeptide epitope.

An antibody, oligopeptide or other organic molecule that “inhibits thegrowth of tumor cells expressing a TAT polypeptide” or a “growthinhibitory” antibody, oligopeptide or other organic molecule is onewhich results in measurable growth inhibition of cancer cells expressingor overexpressing the appropriate TAT polypeptide. The TAT polypeptidemay be a transmembrane polypeptide expressed on the surface of a cancercell or may be a polypeptide that is produced and secreted by a cancercell. Preferred growth inhibitory anti-TAT antibodies, oligopeptides ororganic molecules inhibit growth of TAT-expressing tumor cells bygreater than 20%, preferably from about 20% to about 50%, and even morepreferably, by greater than 50% (e.g., from about 50% to about 100%) ascompared to the appropriate control, the control typically being tumorcells not treated with the antibody, oligopeptide or other organicmolecule being tested. In one embodiment, growth inhibition can bemeasured at an antibody concentration of about 0.1 to 30 μg/ml or about0.5 nM to 200 nM in cell culture, where the growth inhibition isdetermined 1-10 days after exposure of the tumor cells to the antibody.Growth inhibition of tumor cells in vivo can be determined in variousways such as is described in the Experimental Examples section below.The antibody is growth inhibitory in vivo if administration of theanti-TAT antibody at about 1 μg/kg to about 100 mg/kg body weightresults in reduction in tumor size or tumor cell proliferation withinabout 5 days to 3 months from the first administration of the antibody,preferably within about 5 to 30 days.

An antibody, oligopeptide or other organic molecule which “inducesapoptosis” is one which induces programmed cell death as determined bybinding of annexin V, fragmentation of DNA, cell shrinkage, dilation ofendoplasmic reticulum, cell fragmentation, and/or formation of membranevesicles (called apoptotic bodies). The cell is usually one whichoverexpresses a TAT polypeptide. Preferably the cell is a tumor cell,e.g., a prostate, breast, ovarian, stomach, endometrial, lung, kidney,colon, bladder cell. Various methods are available for evaluating thecellular events associated with apoptosis. For example, phosphatidylserine (PS) translocation can be measured by annexin binding; DNAfragmentation can be evaluated through DNA laddering; andnuclear/chromatin condensation along with DNA fragmentation can beevaluated by any increase in hypodiploid cells. Preferably, theantibody, oligopeptide or other organic molecule which induces apoptosisis one which results in about 2 to 50 fold, preferably about 5 to 50fold, and most preferably about 10 to 50 fold, induction of annexinbinding relative to untreated cell in an annexin binding assay.

Antibody “effector functions” refer to those biological activitiesattributable to the Fc region (a native sequence Fc region or amino acidsequence variant Fc region) of an antibody, and vary with the antibodyisotype. Examples of antibody effector functions include: C1q bindingand complement dependent cytotoxicity; Fc receptor binding;antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; downregulation of cell surface receptors (e.g., B cell receptor); and B cellactivation.

“Antibody-dependent cell-mediated cytotoxicity” or “ADCC” refers to aform of cytotoxicity in which secreted Ig bound onto Fc receptors (FcRs)present on certain cytotoxic cells (e.g., Natural Killer (NK) cells,neutrophils, and macrophages) enable these cytotoxic effector cells tobind specifically to an antigen-bearing target cell and subsequentlykill the target cell with cytotoxins. The antibodies “arm” the cytotoxiccells and are absolutely required for such killing. The primary cellsfor mediating ADCC, NK cells, express FcγRIII only, whereas monocytesexpress FcγRI, FcγRII and FcγRIII. FcR expression on hematopoietic cellsis summarized in Table 3 on page 464 of Ravetch and Kinet, Annu. Rev.Immunol. 9:457-92 (1991). To assess ADCC activity of a molecule ofinterest, an in vitro ADCC assay, such as that described in U.S. Pat.No. 5,500,362 or 5,821,337 may be performed. Useful effector cells forsuch assays include peripheral blood mononuclear cells (PBMC) andNatural Killer (NK) cells. Alternatively, or additionally, ADCC activityof the molecule of interest may be assessed in vivo, e.g., in a animalmodel such as that disclosed in Clynes et al. (USA) 95:652-656 (1998).

“Fc receptor” or “FcR” describes a receptor that binds to the Fc regionof an antibody. The preferred FcR is a native sequence human FcR.Moreover, a preferred FcR is one which binds an IgG antibody (a gammareceptor) and includes receptors of the FcγRI, FcγRII and FcγRIIIsubclasses, including allelic variants and alternatively spliced formsof these receptors. FcγRII receptors include FcγRIIA (an “activatingreceptor”) and FcγRIIB (an “inhibiting receptor”), which have similaramino acid sequences that differ primarily in the cytoplasmic domainsthereof. Activating receptor FcγRIIA contains an immunoreceptortyrosine-based activation motif (ITAM) in its cytoplasmic domain.Inhibiting receptor FcγRIIB contains an immunoreceptor tyrosine-basedinhibition motif (ITIM) in its cytoplasmic domain. (see review M. inDaëron, Annu. Rev. Immunol. 15:203-234 (1997)). FcRs are reviewed inRavetch and Kinet, Annu. Rev. Immunol. 9:457-492 (1991); Capel et al.,Immunomethods 4:25-34 (1994); and de Haas et al., J. Lab. Clin. Med.126:330-41 (1995). Other FcRs, including those to be identified in thefuture, are encompassed by the term “FcR” herein. The term also includesthe neonatal receptor, FcRn, which is responsible for the transfer ofmaternal IgGs to the fetus (Guyer et al., J. Immunol. 117:587 (1976) andKim et al., J. Immunol. 24:249 (1994)).

“Human effector cells” are leukocytes which express one or more FcRs andperform effector functions. Preferably, the cells express at leastFcγRIII and perform ADCC effector function. Examples of human leukocyteswhich mediate ADCC include peripheral blood mononuclear cells (PBMC),natural killer (NK) cells, monocytes, cytotoxic T cells and neutrophils;with PBMCs and NK cells being preferred. The effector cells may beisolated from a native source, e.g., from blood.

“Complement dependent cytotoxicity” or “CDC” refers to the lysis of atarget cell in the presence of complement. Activation of the classicalcomplement pathway is initiated by the binding of the first component ofthe complement system (C1q) to antibodies (of the appropriate subclass)which are bound to their cognate antigen. To assess complementactivation, a CDC assay, e.g., as described in Gazzano-Santoro et al.,J. Immunol. Methods 202:163 (1996), may be performed.

The terms “cancer” and “cancerous” refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth. Examples of cancer include, but are not limitedto, carcinoma, lymphoma, blastoma, sarcoma, and leukemia or lymphoidmalignancies. More particular examples of such cancers include squamouscell cancer (e.g., epithelial squamous cell cancer), lung cancerincluding small-cell lung cancer, non-small cell lung cancer,adenocarcinoma of the lung and squamous carcinoma of the lung, cancer ofthe peritoneum, hepatocellular cancer, gastric or stomach cancerincluding gastrointestinal cancer, pancreatic cancer, glioblastoma,cervical cancer, ovarian cancer, liver cancer, bladder cancer, cancer ofthe urinary tract, hepatoma, breast cancer, colon cancer, rectal cancer,colorectal cancer, endometrial or uterine carcinoma, salivary glandcarcinoma, kidney or renal cancer, prostate cancer, vulval cancer,thyroid cancer, hepatic carcinoma, anal carcinoma, penile carcinoma,melanoma, multiple myeloma and B-cell lymphoma, brain, as well as headand neck cancer, and associated metastases.

The terms “cell proliferative disorder” and “proliferative disorder”refer to disorders that are associated with some degree of abnormal cellproliferation. In one embodiment, the cell proliferative disorder iscancer.

“Tumor”, as used herein, refers to all neoplastic cell growth andproliferation, whether malignant or benign, and all pre-cancerous andcancerous cells and tissues.

An antibody, oligopeptide or other organic molecule which “induces celldeath” is one which causes a viable cell to become nonviable. The cellis one which expresses a TAT polypeptide, preferably a cell thatoverexpresses a TAT polypeptide as compared to a normal cell of the sametissue type. The TAT polypeptide may be a transmembrane polypeptideexpressed on the surface of a cancer cell or may be a polypeptide thatis produced and secreted by a cancer cell. Preferably, the cell is acancer cell, e.g., a breast, ovarian, stomach, endometrial, salivarygland, lung, kidney, colon, thyroid, pancreatic or bladder cell. Celldeath in vitro may be determined in the absence of complement and immuneeffector cells to distinguish cell death induced by antibody-dependentcell-mediated cytotoxicity (ADCC) or complement dependent cytotoxicity(CDC). Thus, the assay for cell death may be performed using heatinactivated serum (i.e., in the absence of complement) and in theabsence of immune effector cells. To determine whether the antibody,oligopeptide or other organic molecule is able to induce cell death,loss of membrane integrity as evaluated by uptake of propidium iodide(PI), trypan blue (see Moore et al. Cytotechnology 17:1-11 (1995)) or7AAD can be assessed relative to untreated cells. Preferred celldeath-inducing antibodies, oligopeptides or other organic molecules arethose which induce PI uptake in the PI uptake assay in BT474 cells.

A “TAT-expressing cell” is a cell which expresses an endogenous ortransfected TAT polypeptide either on the cell surface or in a secretedform. A “TAT-expressing cancer” is a cancer comprising cells that have aTAT polypeptide present on the cell surface or that produce and secretea TAT polypeptide. A “TAT-expressing cancer” optionally producessufficient levels of TAT polypeptide on the surface of cells thereof,such that an anti-TAT antibody, oligopeptide ot other organic moleculecan bind thereto and have a therapeutic effect with respect to thecancer. In another embodiment, a “TAT-expressing cancer” optionallyproduces and secretes sufficient levels of TAT polypeptide, such that ananti-TAT antibody, oligopeptide ot other organic molecule antagonist canbind thereto and have a therapeutic effect with respect to the cancer.With regard to the latter, the antagonist may be an antisenseoligonucleotide which reduces, inhibits or prevents production andsecretion of the secreted TAT polypeptide by tumor cells. A cancer which“overexpresses” a TAT polypeptide is one which has significantly higherlevels of TAT polypeptide at the cell surface thereof, or produces andsecretes, compared to a noncancerous cell of the same tissue type. Suchoverexpression may be caused by gene amplification or by increasedtranscription or translation. TAT polypeptide overexpression may bedetermined in a diagnostic or prognostic assay by evaluating increasedlevels of the TAT protein present on the surface of a cell, or secretedby the cell (e.g., via an immunohistochemistry assay using anti-TATantibodies prepared against an isolated TAT polypeptide which may beprepared using recombinant DNA technology from an isolated nucleic acidencoding the TAT polypeptide; FACS analysis, etc.). Alternatively, oradditionally, one may measure levels of TAT polypeptide-encoding nucleicacid or mRNA in the cell, e.g., via fluorescent in situ hybridizationusing a nucleic acid based probe corresponding to a TAT-encoding nucleicacid or the complement thereof; (FISH; see WO98/45479 published October,1998), Southern blotting, Northern blotting, or polymerase chainreaction (PCR) techniques, such as real time quantitative PCR(RT-PCR).One may also study TAT polypeptide overexpression by measuring shedantigen in a biological fluid such as serum, e.g, using antibody-basedassays (see also, e.g., U.S. Pat. No. 4,933,294 issued Jun. 12, 1990;WO91/05264 published Apr. 18, 1991; U.S. Pat. No. 5,401,638 issued Mar.28, 1995; and Sias et al., J. Immunol. Methods 132:73-80 (1990)). Asidefrom the above assays, various in vivo assays are available to theskilled practitioner. For example, one may expose cells within the bodyof the patient to an antibody which is optionally labeled with adetectable label, e.g., a radioactive isotope, and binding of theantibody to cells in the patient can be evaluated, e.g., by externalscanning for radioactivity or by analyzing a biopsy taken from a patientpreviously exposed to the antibody.

As used herein, the term “immunoadhesin” designates antibody-likemolecules which combine the binding specificity of a heterologousprotein (an “adhesin”) with the effector functions of immunoglobulinconstant domains. Structurally, the immunoadhesins comprise a fusion ofan amino acid sequence with the desired binding specificity which isother than the antigen recognition and binding site of an antibody(i.e., is “heterologous”), and an immunoglobulin constant domainsequence. The adhesin part of an immunoadhesin molecule typically is acontiguous amino acid sequence comprising at least the binding site of areceptor or a ligand. The immunoglobulin constant domain sequence in theimmunoadhesin may be obtained from any immunoglobulin, such as IgG-1,IgG-2, IgG-3, or IgG-4 subtypes, IgA (including IgA-1 and IgA-2), IgE,IgD or IgM.

The word “label” when used herein refers to a detectable compound orcomposition which is conjugated directly or indirectly to the antibody,oligopeptide or other organic molecule so as to generate a “labeled”antibody, oligopeptide or other organic molecule. The label may bedetectable by itself (e.g. radioisotope labels or fluorescent labels)or, in the case of an enzymatic label, may catalyze chemical alterationof a substrate compound or composition which is detectable.

The term “cytotoxic agent” as used herein refers to a substance thatinhibits or prevents the function of cells and/or causes destruction ofcells. The term is intended to include radioactive isotopes (e.g.,At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³² and radioactiveisotopes of Lu), chemotherapeutic agents e.g. methotrexate, adriamicin,vinca alkaloids (vincristine, vinblastine, etoposide), doxorubicin,melphalan, mitomycin C, chlorambucil, daunorubicin or otherintercalating agents, enzymes and fragments thereof such as nucleolyticenzymes, antibiotics, and toxins such as small molecule toxins orenzymatically active toxins of bacterial, fungal, plant or animalorigin, including fragments and/or variants thereof, and the variousantitumor or anticancer agents disclosed below. Other cytotoxic agentsare described below. A tumoricidal agent causes destruction of tumorcells.

A “growth inhibitory agent” when used herein refers to a compound orcomposition which inhibits growth of a cell, especially a TAT-expressingcancer cell, either in vitro or in vivo. Thus, the growth inhibitoryagent may be one which significantly reduces the percentage ofTAT-expressing cells in S phase. Examples of growth inhibitory agentsinclude agents that block cell cycle progression (at a place other thanS phase), such as agents that induce G1 arrest and M-phase arrest.Classical M-phase blockers include the vincas (vincristine andvinblastine), taxanes, and topoisomerase II inhibitors such asdoxorubicin, epirubicin, daunorubicin, etoposide, and bleomycin. Thoseagents that arrest G1 also spill over into S-phase arrest, for example,DNA alkylating agents such as tamoxifen, prednisone, dacarbazine,mechlorethamine, cisplatin, methotrexate, 5-fluorouracil, and ara-C.Further information can be found in The Molecular Basis of Cancer,Mendelsohn and Israel, eds., Chapter 1, entitled “Cell cycle regulation,oncogenes, and antineoplastic drugs” by Murakami et al. (WB Saunders:Philadelphia, 1995), especially p. 13. The taxanes (paclitaxel anddocetaxel) are anticancer drugs both derived from the yew tree.Docetaxel (TAXOTERE®, Rhone-Poulenc Rorer), derived from the Europeanyew, is a semisynthetic analogue of paclitaxel (TAXOL®, Bristol-MyersSquibb). Paclitaxel and docetaxel promote the assembly of microtubulesfrom tubulin dimers and stabilize microtubules by preventingdepolymerization, which results in the inhibition of mitosis in cells.

“Doxorubicin” is an anthracycline antibiotic. The full chemical name ofdoxorubicin is(8S-cis)-10-[(3-amino-2,3,6-trideoxy-α-L-lyxo-hexapyranosyl)oxy]-7,8,9,10-tetrahydro-6,8,11-trihydroxy-8-(hydroxyacetyl)-1-methoxy-5,12-naphthacenedione.

The term “cytokine” is a generic term for proteins released by one cellpopulation which act on another cell as intercellular mediators.Examples of such cytokines are lymphokines, monokines, and traditionalpolypeptide hormones. Included among the cytokines are growth hormonesuch as human growth hormone, N-methionyl human growth hormone, andbovine growth hormone; parathyroid hormone; thyroxine; insulin;proinsulin; relaxin; prorelaxin; glycoprotein hormones such as folliclestimulating hormone (FSH), thyroid stimulating hormone (TSH), andluteinizing hormone (LH); hepatic growth factor; fibroblast growthfactor; prolactin; placental lactogen; tumor necrosis factor-α and -β;mullerian-inhibiting substance; mouse gonadotropin-associated peptide;inhibin; activin; vascular endothelial growth factor; integrin;thrombopoietin (TPO); nerve growth factors such as NGF-β;platelet-growth factor; transforming growth factors (TGFs) such as TGF-αand TGF-β; insulin-like growth factor-I and -II; erythropoietin (EPO);osteoinductive factors; interferons such as interferon-α, -β, and -γ;colony stimulating factors (CSFs) such as macrophage-CSF (M-CS F);granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF (G-CSF);interleukins (ILs) such as IL-1, IL-1a, IL-2, IL-3, IL-4, IL-5, IL-6,IL-7, IL-8, IL-9, IL-11, IL-12; a tumor necrosis factor such as TNF-α orTNF-β; and other polypeptide factors including LIF and kit ligand (KL).As used herein, the term cytokine includes proteins from natural sourcesor from recombinant cell culture and biologically active equivalents ofthe native sequence cytokines.

The term “package insert” is used to refer to instructions customarilyincluded in commercial packages of therapeutic products, that containinformation about the indications, usage, dosage, administration,contraindications and/or warnings concerning the use of such therapeuticproducts.

TABLE 1 /*  *  * C-C increased from 12 to 15  * Z is average of EQ  * Bis average of ND  * match with stop is _M; stop-stop = 0; J (joker)match = 0  */ #define _M −8 /* value of a match with a stop */ int_day[26][26] = { /* A B C D E F G H I J K L M N O P Q R S T U V W X Y Z*/ /* A */ { 2, 0,−2, 0, 0,−4, 1,−1,−1, 0,−1,−2,−1, 0,_M, 1, 0,−2, 1, 1,0, 0,−6, 0,−3, 0}, /* B */ { 0, 3,−4, 3, 2,−5, 0, 1,−2, 0, 0,−3,−2,2,_M,−1, 1, 0, 0, 0, 0,−2,−5, 0,−3, 1}, /* C */{−2,−4,15,−5,−5,−4,−3,−3,−2, 0,−5,−6,−5,−4,_M,−3,−5,−4, 0,−2, 0,−2,−8,0, 0,−5}, /* D */ { 0, 3,−5, 4, 3,−6, 1, 1,−2, 0, 0,−4,−3, 2,_M,−1,2,−1, 0, 0, 0,−2,−7, 0,−4, 2}, /* E */ { 0, 2,−5, 3, 4,−5, 0, 1,−2, 0,0,−3,−2, 1,_M,−1, 2,−1, 0, 0, 0,−2,−7, 0,−4, 3}, /* F */{−4,−5,−4,−6,−5, 9,−5,−2, 1, 0,−5, 2, 0,−4,_M,−5,−5,−4,−3,−3, 0,−1, 0,0, 7,−5}, /* G */ { 1, 0,−3, 1, 0,−5, 5,−2,−3, 0,−2,−4,−3,0,_M,−1,−1,−3, 1, 0, 0,−1,−7, 0,−5, 0}, /* H */ {−1, 1,−3, 1, 1,−2,−2,6,−2, 0, 0,−2,−2, 2,_M, 0, 3, 2,−1,−1, 0,−2,−3, 0, 0, 2}, /* I */{−1,−2,−2,−2,−2, 1,−3,−2, 5, 0,−2, 2, 2,−2,_M,−2,−2,−2,−1, 0, 0, 4,−5,0,−1,−2}, /* J */ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0,0, 0, 0, 0, 0, 0, 0, 0, 0}, /* K */ {−1, 0,−5, 0, 0,−5,−2, 0,−2, 0,5,−3, 0, 1,_M,−1, 1, 3, 0, 0, 0,−2,−3, 0,−4, 0}, /* L */{−2,−3,−6,−4,−3, 2,−4,−2, 2, 0,−3, 6, 4,−3,_M,−3,−2,−3,−3,−1, 0, 2,−2,0,−1,−2}, /* M */ {−1,−2,−5,−3,−2, 0,−3,−2, 2, 0, 0, 4, 6,−2,_M,−2,−1,0,−2,−1, 0, 2,−4, 0,−2,−1}, /* N */ { 0, 2,−4, 2, 1,−4, 0, 2,−2, 0,1,−3,−2, 2,_M,−1, 1, 0, 1, 0, 0,−2,−4, 0,−2, 1}, /* O */{_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,0,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M,_M}, /* P */ { 1,−1,−3,−1,−1,−5,−1,0,−2, 0,−1,−3,−2,−1,_M, 6, 0, 0, 1, 0, 0,−1,−6, 0,−5, 0}, /* Q */ { 0,1,−5, 2, 2,−5,−1, 3,−2, 0, 1,−2,−1, 1,_M, 0, 4, 1,−1,−1, 0,−2,−5, 0,−4,3}, /* R */ {−2, 0,−4,−1,−1,−4,−3, 2,−2, 0, 3,−3, 0, 0,_M, 0, 1, 6,0,−1, 0,−2, 2, 0,−4, 0}, /* S */ { 1, 0, 0, 0, 0,−3, 1,−1,−1, 0,0,−3,−2, 1,_M, 1,−1, 0, 2, 1, 0,−1,−2, 0,−3, 0}, /* T */ { 1, 0,−2, 0,0,−3, 0,−1, 0, 0, 0,−1,−1, 0,_M, 0,−1,−1, 1, 3, 0, 0,−5, 0,−3, 0}, /* U*/ { 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0, 0, 0, 0, 0, 0,0, 0, 0, 0}, /* V */ { 0,−2,−2,−2,−2,−1,−1,−2, 4, 0,−2, 2,2,−2,_M,−1,−2,−2,−1, 0, 0, 4,−6, 0,−2,−2}, /* W */ {−6,−5,−8,−7,−7,0,−7,−3,−5, 0,−3,−2,−4,−4,_M,−6,−5, 2,−2,−5, 0,−6,17, 0, 0,−6}, /* X */{ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,_M, 0, 0, 0, 0, 0, 0, 0, 0,0, 0, 0}, /* Y */ {−3,−3, 0,−4,−4, 7,−5, 0,−1,0,−4,−1,−2,−2,_M,−5,−4,−4,−3,−3, 0,−2, 0, 0,10,−4}, /* Z */ { 0, 1,−5,2, 3,−5, 0, 2,−2, 0, 0,−2,−1, 1,_M, 0, 3, 0, 0, 0, 0,−2,−6, 0,−4, 4} };/*  */ #include <stdio.h> #include <ctype.h> #define MAXJMP 16 /* maxjumps in a diag */ #define MAXGAP 24 /* don't continue to penalize gapslarger than this */ #define JMPS 1024 /* max jmps in an path */ #defineMX 4 /* save if there's at least MX−1 bases since last jmp */ #defineDMAT 3 /* value of matching bases */ #define DMIS 0 /* penalty formismatched bases */ #define DINS0 8 /* penalty for a gap */ #defineDINS1 1 /* penalty per base */ #define PINS0 8 /* penalty for a gap */#define PINS1 4 /* penalty per residue */ struct jmp { short n[MAXJMP];/* size of jmp (neg for dely) */ unsigned short x[MAXJMP]; /* base no.of jmp in seq x */ }; /* limits seq to 2{circumflex over ( )}16 −1 */struct diag { int score; /* score at last jmp */ long offset; /* offsetof prev block */ short ijmp; /* current jmp index */ struct jmp jp; /*list of jmps */ }; struct path { int spc; /* number of leading spaces */short n[JMPS];/* size of jmp (gap) */ int x[JMPS];/* loc of jmp (lastelem before gap) */ }; char *ofile; /* output file name */ char*namex[2]; /* seq names: getseqs( ) */ char *prog; /* prog name for errmsgs */ char *seqx[2]; /* seqs: getseqs( ) */ int dmax; /* best diag:nw( ) */ int dmax0; /* final diag */ int dna; /* set if dna: main( ) */int endgaps; /* set if penalizing end gaps */ int gapx, gapy; /* totalgaps in seqs */ int len0, len1; /* seq lens */ int ngapx, ngapy; /*total size of gaps */ int smax; /* max score: nw( ) */ int *xbm; /*bitmap for matching */ long offset; /* current offset in jmp file */struct diag *dx; /* holds diagonals */ struct path pp[2]; /* holds pathfor seqs */ char *calloc( ), *malloc( ), *index( ), *strcpy( ); char*getseq( ), *g_calloc( ); /* Needleman-Wunsch alignment program  *  *usage: progs file1 file2  * where file1 and file2 are two dna or twoprotein sequences.  * The sequences can be in upper- or lower-case anmay contain ambiguity  * Any lines beginning with ‘;’, ‘>’ or ‘<’ areignored  * Max file length is 65535 (limited by unsigned short x in thejmp struct)  * A sequence with ⅓ or more of its elements ACGTU isassumed to be DNA  * Output is in the file “align.out”  *  * The programmay create a tmp file in /tmp to hold info about traceback.  * Originalversion developed under BSD 4.3 on a vax 8650  */ #include “nw.h”#include “day.h” static _dbval[26] = {1,14,2,13,0,0,4,11,0,0,12,0,3,15,0,0,0,5,6,8,8,7,9,0,10,0 }; static_pbval[26] = { 1, 2|(1<<(‘D’-‘A’))|(1<<(‘N’-‘A’)), 4, 8, 16, 32, 64,128, 256, 0xFFFFFFF, 1<<10, 1<<11, 1<<12, 1<<13, 1<<14, 1<<15, 1<<16,1<<17, 1<<18, 1<<19, 1<<20, 1<<21, 1<<22, 1<<23, 1<<24,1<<25|(1<<(‘E’-‘A’))|(1<<(‘Q’-‘A’)) }; main(ac, av) main int ac; char*av[ ]; { prog = av[0]; if (ac != 3) { fprintf(stderr,“usage: %s file1file2\n”, prog); fprintf(stderr,“where file1 and file2 are two dna ortwo protein sequences.\n”); fprintf(stderr,“The sequences can be inupper- or lower-case\n”); fprintf(stderr,“Any lines beginning with ‘;’or ‘<’ are ignored\n”); fprintf(stderr,“Output is in the file\”align.out\“\n”); exit(1); } namex[0] = av[1]; namex[1] = av[2];seqx[0] = getseq(namex[0], &len0); seqx[1] = getseq(namex[1], &len1);xbm = (dna)? _dbval : _pbval; endgaps = 0; /* 1 to penalize endgaps */ofile = “align.out”; /* output file */ nw( ); /* fill in the matrix, getthe possible jmps */ readjmps( ); /* get the actual jmps */ print( ); /*print stats, alignment */ cleanup(0); /* unlink any tmp files */ } /* dothe alignment, return best score: main( )  * dna: values in Fitch andSmith, PNAS, 80, 1382-1386, 1983  * pro: PAM 250 values  * When scoresare equal, we prefer mismatches to any gap, prefer  * a new gap toextending an ongoing gap, and prefer a gap in seqx  * to a gap in seq y. */ nw( ) nw { char *px, *py; /* seqs and ptrs */ int *ndely, *dely; /*keep track of dely */ int ndelx, delx; /* keep track of delx */ int*tmp; /* for swapping row0, row1 */ int mis; /* score for each type */int ins0, ins1; /* insertion penalties */ register id; /* diagonal index*/ register ij; /* jmp index */ register *col0, *col1; /* score forcurr, last row */ register xx, yy; /* index into seqs */ dx = (structdiag *)g_calloc(“to get diags”, len0+len1+1, sizeof(struct diag)); ndely= (int *)g_calloc(“to get ndely”, len1+1, sizeof(int)); dely = (int*)g_calloc(“to get dely”, len1+1, sizeof(int)); col0 = (int*)g_calloc(“to get col0”, len1+1, sizeof(int)); col1 = (int*)g_calloc(“to get col1”, len1+1, sizeof(int)); ins0 = (dna)? DINS0 :PINS0; ins1 = (dna)? DINS1 : PINS1; smax = −10000; if (endgaps) { for(col0[0] = dely[0] = −ins0, yy = 1; yy <= len1; yy++) { col0[yy] =dely[yy] = col0[yy−1] − ins1; ndely[yy] = yy; } col0[0] = 0; /* WatermanBull Math Biol 84 */ } else for (yy = 1; yy <= len1; yy++) dely[yy] =−ins0; /* fill in match matrix  */ for (px = seqx[0], xx = 1; xx <=len0; px++, xx++) { /* initialize first entry in col  */ if (endgaps) {if (xx == 1) col1[0] = delx = −(ins0+ins1); else col1[0] = delx =col0[0] − ins1; ndelx = xx; } else { col1[0] = 0; delx = −ins0; ndelx =0; } ...nw for (py = seqx[1], yy = 1; yy <= len1; py++, yy++) { mis =col0[yy−1]; if (dna) mis += (xbm[*px−‘A’]&xbm[*py−‘A’])? DMAT : DMIS;else mis += _day[*px−‘A’][*py−‘A’]; /* update penalty for del in x seq; * favor new del over ongong del  * ignore MAXGAP if weighting endgaps */ if (endgaps || ndely[yy] < MAXGAP) { if (col0[yy] − ins0 >=dely[yy]) { dely[yy] = col0[yy] − (ins0+ins1); ndely[yy] = 1; } else {dely[yy] −= ins1; ndely[yy]++; } } else { if (col0[yy] − (ins0+ins1) >=dely[yy]) { dely[yy] = col0[yy] − (ins0+ins1); ndely[yy] = 1; } elsendely[yy]++; } /* update penalty for del in y seq;  * favor new del overongong del  */ if (endgaps || ndelx < MAXGAP) { if (col1[yy−1] − ins0 >=delx) { delx = col1[yy−1] − (ins0+ins1); ndelx = 1; } else { delx −=ins1; ndelx++; } } else { if (col1[yy−1] − (ins0+ins1) >= delx) { delx =col1[yy−1] − (ins0+ins1); ndelx = 1; } else ndelx++; } /* pick themaximum score; we're favoring  * mis over any del and delx over dely  */...nw id = xx − yy + len1 − 1; if (mis >= delx && mis >= dely[yy])col1[yy] = mis; else if (delx >= dely[yy]) { col1[yy] = delx; ij =dx[id].ijmp; if (dx[id].jp.n[0] && (!dna || (ndelx >= MAXJMP && xx >dx[id].jp.x[ij]+MX) || mis > dx[id].score+DINS0)) { dx[id].ijmp++; if(++ij >= MAXJMP) { writejmps(id); ij = dx[id].ijmp = 0; dx[id].offset =offset; offset += sizeof(struct jmp) + sizeof(offset); } }dx[id].jp.n[ij] = ndelx; dx[id].jp.x[ij] = xx; dx[id].score = delx; }else { col1[yy] = dely[yy]; ij = dx[id].ijmp; if (dx[id].jp.n[0] &&(!dna || (ndely[yy] >= MAXJMP && xx > dx[id].jp.x[ij]+MX) || mis >dx[id].score+DINS0)) { dx[id].ijmp++; if (++ij >= MAXJMP) {writejmps(id); ij = dx[id].ijmp = 0; dx[id].offset = offset; offset +=sizeof(struct jmp) + sizeof(offset); } } dx[id].jp.n[ij] = −ndely[yy];dx[id].jp.x[ij] = xx; dx[id].score = dely[yy]; } if (xx == len0 && yy <len1) { /* last col  */ if (endgaps) col1[yy] −= ins0+ins1*(len1−yy); if(col1[yy] > smax) { smax = col1[yy]; dmax = id; } } } if (endgaps && xx< len0) col1[yy−1] −= ins0+ins1*(len0−xx); if (col1[yy−1] > smax) { smax= col1[yy−1]; dmax = id; } tmp = col0; col0 = col1; col1 = tmp; } (void)free((char *)ndely); (void) free((char *)dely); (void) free((char*)col0); (void) free((char *)col1); } /*  *  * print( ) -- only routinevisible outside this module  *  * static:  * getmat( ) -- trace backbest path, count matches: print( )  * pr_align( ) -- print alignment ofdescribed in array p[ ]: print( )  * dumpblock( ) -- dump a block oflines with numbers, stars: pr_align( )  * nums( ) -- put out a numberline: dumpblock( )  * putline( ) -- put out a line (name, [num], seq,[num]): dumpblock( )  * stars( ) - -put a line of stars: dumpblock( )  *stripname( ) -- strip any path and prefix from a seqname  */ #include“nw.h” #define SPC 3 #define P_LINE 256 /* maximum output line */#define P_SPC 3 /* space between name or num and seq */ extern_day[26][26]; int olen; /* set output line length */ FILE *fx; /* outputfile */ print( ) print { int lx, ly, firstgap, lastgap; /* overlap */ if((fx = fopen(ofile, “w”)) == 0) { fprintf(stderr,“ %s: can't write%s\n”, prog, ofile); cleanup(1); } fprintf(fx, “<first sequence: %s(length = %d)\n”, namex[0], len0); fprintf(fx, “<second sequence: %s(length = %d)\n”, namex[1], len1); olen = 60; lx = len0; ly = len1;firstgap = lastgap = 0; if (dmax < len1 − 1) { /* leading gap in x */pp[0].spc = firstgap = len1 − dmax − 1; ly −= pp[0].spc; } else if(dmax > len1 − 1) { /* leading gap in y */ pp[1].spc = firstgap = dmax −(len1 − 1); lx −= pp[1].spc; } if (dmax0 < len0 − 1) { /* trailing gapin x */ lastgap = len0 − dmax0 −1; lx −= lastgap; } else if (dmax0 >len0 − 1) { /* trailing gap in y */ lastgap = dmax0 − (len0 − 1); ly −=lastgap; } getmat(lx, ly, firstgap, lastgap); pr_align( ); } /*  * traceback the best path, count matches  */ static getmat(lx, ly, firstgap,lastgap) getmat int lx, ly; /* “core” (minus endgaps) */ int firstgap,lastgap; /* leading trailing overlap */ { int nm, i0, i1, siz0, siz1;char outx[32]; double pct; register n0, n1; register char *p0, *p1; /*get total matches, score  */ i0 = i1 = siz0 = siz1 = 0; p0 = seqx[0] +pp[1].spc; p1 = seqx[1] + pp[0].spc; n0 = pp[1].spc + 1; n1 =pp[0].spc + 1; nm = 0; while ( *p0 && *p1 ) { if (siz0) { p1++; n1++;siz0−−; } else if (siz1) { p0++; n0++; siz1−−; } else { if(xbm[*p0−‘A’]&xbm[*p1−‘A’]) nm++; if (n0++ == pp[0].x[i0]) siz0 =pp[0].n[i0++]; if (n1++ == pp[1].x[i1]) siz1 = pp[1].n[i1++]; p0++;p1++; } } /* pct homology:  * if penalizing endgaps, base is the shorterseq  * else, knock off overhangs and take shorter core  */ if (endgaps)lx = (len0 < len1)? len0 : len1; else lx = (lx < ly)? lx : ly; pct =100.*(double)nm/(double)lx; fprintf(fx, “\n”); fprintf(fx, “<%d match%sin an overlap of %d: %.2f percent similarity\n”, nm, (nm == 1)? ““ :“es”, lx, pct); fprintf(fx, “<gaps in first sequence: %d”, gapx);...getmat if (gapx) { (void) sprintf(outx, “ (%d %s%s)”, ngapx, (dna)?“base”:“residue”, (ngapx == 1)? “”:“s”); fprintf(fx,“%s”, outx);fprintf(fx, “, gaps in second sequence: %d”, gapy); if (gapy) { (void)sprintf(outx, “ (%d %s%s)”, ngapy, (dna)? “base”:“residue”, (ngapy ==1)? “”:“s”); fprintf(fx,“%s”, outx); } if (dna) fprintf(fx, “\n<score:%d (match = %d, mismatch = %d, gap penalty = %d + %d per base)\n”, smax,DMAT, DMIS, DINS0, DINS1); else fprintf(fx, “\n<score: %d (Dayhoff PAM250 matrix, gap penalty = %d + %d per residue)\n”, smax, PINS0, PINS1);if (endgaps) fprintf(fx, “<endgaps penalized. left endgap: %d %s%s,right endgap: %d %s%s\n”, firstgap, (dna)? “base” : “residue”, (firstgap== 1)? “” : “s”, lastgap, (dna)? “base” : “residue”, (lastgap == 1)? “”: “s”); else fprintf(fx, “<endgaps not penalized\n”); } static nm; /*matches in core -- for checking */ static lmax; /* lengths of strippedfile names */ static ij[2]; /* jmp index for a path */ static nc[2]; /*number at start of current line */ static ni[2]; /* current elem number-- for gapping */ static siz[2]; static char *ps[2]; /* ptr to currentelement */ static char *po[2]; /* ptr to next output char slot */ staticchar out[2][P_LINE]; /* output line */ static char star[P_LINE]; /* setby stars( ) */ /*  * print alignment of described in struct path pp[ ] */ static pr_align( ) pr_align { int nn; /* char count */ int more;register i; for (i = 0, lmax = 0; i < 2; i++) { nn =stripname(namex[i]); if (nn > lmax) lmax = nn; nc[i] = 1; ni[i] = 1;siz[i] = ij[i] = 0; ps[i] = seqx[i]; po[i] = out[i]; } for (nn = nm = 0,more = 1; more; ) { ...pr_align for (i = more = 0; i < 2; i++) { /*  *do we have more of this sequence?  */ if (!*ps[i]) continue; more++; if(pp[i].spc) { /* leading space */ *po[i]++ = ‘ ’; pp[i].spc−−; } else if(siz[i]) { /* in a gap */ *po[i]++ = ‘-’; siz[i]−−; } else { /* we'reputting a seq element  */ *po[i] = *ps[i]; if (islower(*ps[i])) *ps[i] =toupper(*ps[i]); po[i]++; ps[i]++; /*  * are we at next gap for thisseq?  */ if (ni[i] == pp[i].x[ij[i]]) { /*  * we need to merge all gaps * at this location  */ siz[i] = pp[i].n[ij[i]++]; while (ni[i] ==pp[i].x[ij[i]]) siz[i] += pp[i].n[ij[i]++]; } ni[i]++; } } if (++nn ==olen || !more && nn) { dumpblock( ); for (i = 0; i < 2; i++) po[i] =out[i]; nn = 0; } } } /*  * dump a block of lines, including numbers,stars: pr_align( )  */ static dumpblock( ) dumpblock { register i; for(i = 0; i < 2; i++) *po[i]−− = ‘\0’; ...dumpblock (void) putc(‘\n’, fx);for (i = 0; i < 2; i++) { if (*out[i] && (*out[i] != ‘ ’ || *(po[i]) !=‘ ’)) { if (i == 0) nums(i); if (i == 0 && *out[1]) stars( );putline(i); if (i == 0 && *out[1]) fprintf(fx, star); if (i == 1)nums(i); } } } /*  * put out a number line: dumpblock( )  */ staticnums(ix) nums int ix; /* index in out[ ] holding seq line */ { charnline[P_LINE]; register i, j; register char *pn, *px, *py; for (pn =nline, i = 0; i < lmax+P_SPC; i++, pn++) *pn = ‘ ’; for (i = nc[ix], py= out[ix]; *py; py++, pn++) { if (*py == ‘ ’ || *py == ‘-’) *pn = ‘ ’;else { if (i%10 == 0 || (i == 1 && nc[ix] != 1)) { j = (i < 0)? −i : i;for (px = pn; j; j /= 10, px−−) *px = j%10 + ‘0’; if (i < 0) *px = ‘-’;} else *pn = ‘ ’; i++; } } *pn = ‘\0’; nc[ix] = i; for (pn = nline; *pn;pn++) (void) putc(*pn, fx); (void) putc(‘\n’, fx); } /*  * put out aline (name, [num], seq, [num]): dumpblock( )  */ static putline(ix)putline int ix; { ...putline int i; register char *px; for (px =namex[ix], i = 0; *px && *px != ‘:’; px++, i++) (void) putc(*px, fx);for (; i < lmax+P_SPC; i++) (void) putc(‘ ’, fx); /* these count from 1: * ni[ ] is current element (from 1)  * nc[ ] is number at start ofcurrent line  */ for (px = out[ix]; *px; px++) (void) putc(*px&0x7F,fx); (void) putc(‘\n’, fx); } /*  * put a line of stars (seqs always inout[0], out[1]): dumpblock( )  */ static stars( ) stars { int i;register char *p0, *p1, cx, *px; if (!*out[0] || (*out[0] == ‘ ’ &&*(po[0]) == ‘ ’) ||  !*out[1] || (*out[1] == ‘ ’ && *(po[1]) == ‘ ’))return; px = star; for (i = lmax+P_SPC; i; i−−) *px++ = ‘ ’; for (p0 =out[0], p1 = out[1]; *p0 && *p1; p0++, p1++) { if (isalpha(*p0) &&isalpha(*p1)) { if (xbm[*p0−‘A’]&xbm[*p1−‘A’]) { cx = ‘*’; nm++; } elseif (!dna && _day[*p0−‘A’][*p1−‘A’] > 0) cx = ‘.’; else cx = ‘ ’; } elsecx = ‘ ’; *px++ = cx; } *px++ = ‘\n’; *px = ‘\0’; } /*  * strip path orprefix from pn, return len: pr_align( )  */ static stripname(pn)stripname char *pn; /* file name (may be path) */ { register char *px,*py; py = 0; for (px = pn; *px; px++) if (*px == ‘/’) py = px + 1; if(py) (void) strcpy(pn, py); return(strlen(pn)); } /*  * cleanup( ) --cleanup any tmp file  * getseq( ) -- read in seq, set dna, len, maxlen * g_calloc( ) -- calloc( ) with error checkin  * readjmps( ) -- get thegood jmps, from tmp file if necessary  * writejmps( ) -- write a filledarray of jmps to a tmp file: nw( )  */ #include “nw.h” #include<sys/file.h> char *jname = “/tmp/homgXXXXXX”; /* tmp file for jmps */FILE *fj; int cleanup( ); /* cleanup tmp file */ long lseek( ); /*  *remove any tmp file if we blow  */ cleanup(i) cleanup int i; { if (fj)(void) unlink(jname); exit(i); } /*  * read, return ptr to seq, set dna,len, maxlen  * skip lines starting with ‘;’, ‘<’, or ‘>’  * seq in upperor lower case  */ char * getseq(file, len) getseq char *file; /* filename */ int *len; /* seq len */ { char line[1024], *pseq; register char*px, *py; int natgc, tlen; FILE *fp; if ((fp = fopen(file,“r”)) == 0) {fprintf(stderr,“%s: can't read %s\n”, prog, file); exit(1); } tlen =natgc = 0; while (fgets(line, 1024, fp)) { if (*line == ‘;’ || *line ==‘<’ || *line == ‘>’) continue; for (px = line; *px != ‘\n’; px++) if(isupper(*px) || islower(*px)) tlen++; } if ((pseq =malloc((unsigned)(tlen+6))) == 0) { fprintf(stderr,“%s: malloc( ) failedto get %d bytes for %s\n”, prog, tlen+6, file); exit(1); } pseq[0] =pseq[1] = pseq[2] = pseq[3] = ‘\0’; ...getseq py = pseq + 4; *len =tlen; rewind(fp); while (fgets(line, 1024, fp)) { if (*line == ‘;’ ||*line == ‘<’ || *line == ‘>’) continue; for (px = line; *px != ‘\n’;px++) { if (isupper(*px)) *py++ = *px; else if (islower(*px)) *py++ =toupper(*px); if (index(“ATGCU”,*(py−1))) natgc++; } } *py++ = ‘\0’; *py= ‘\0’; (void) fclose(fp); dna = natgc > (tlen/3); return(pseq+4); }char * g_calloc(msg, nx, sz) g_calloc char *msg; /* program, callingroutine */ int nx, sz; /* number and size of elements */ { char *px,*calloc( ); if ((px = calloc((unsigned)nx, (unsigned)sz)) == 0) { if(*msg) { fprintf(stderr, “%s: g_calloc( ) failed %s (n=%d, sz=%d)\n”,prog, msg, nx, sz); exit(1); } } return(px); } /*  * get final jmps fromdx[ ] or tmp file, set pp[ ], reset dmax: main( )  */ readjmps( )readjmps { int fd = −1; int siz, i0, i1; register i, j, xx; if (fj) {(void) fclose(fj); if ((fd = open(jname, O_RDONLY, 0)) < 0) {fprintf(stderr, “%s: can't open( ) %s\n”, prog, jname); cleanup(1); } }for (i = i0 = i1 = 0, dmax0 = dmax, xx = len0; ; i++) { while (1) { for(j = dx[dmax].ijmp; j >= 0 && dx[dmax].jp.x[j] >= xx; j−−) ; ...readjmpsif (j < 0 && dx[dmax].offset && fj) { (void) lseek(fd, dx[dmax].offset,0); (void) read(fd, (char *)&dx[dmax].jp, sizeof(struct jmp)); (void)read(fd, (char *)&dx[dmax].offset, sizeof(dx[dmax].offset));dx[dmax].ijmp = MAXJMP−1; } else break; } if (i >= JMPS) {fprintf(stderr, “%s: too many gaps in alignment\n”, prog); cleanup(1); }if (j >= 0) { siz = dx[dmax].jp.n[j]; xx = dx[dmax].jp.x[j]; dmax +=siz; if (siz < 0) { /* gap in second seq */ pp[1].n[i1] = −siz; xx +=siz; /* id = xx − yy + len1 − 1  */ pp[1].x[i1] = xx − dmax + len1 − 1;gapy++; ngapy −= siz; /* ignore MAXGAP when doing endgaps */ siz = (−siz< MAXGAP || endgaps)? −siz : MAXGAP; i1++; } else if (siz > 0) { /* gapin first seq */ pp[0].n[i0] = siz; pp[0].x[i0] = xx; gapx++; ngapx +=siz; /* ignore MAXGAP when doing endgaps */ siz = (siz < MAXGAP ||endgaps)? siz : MAXGAP; i0++; } } else break; } /* reverse the order ofjmps  */ for (j = 0, i0−−; j < i0; j++, i0−−) { i = pp[0].n[j];pp[0].n[j] = pp[0].n[i0]; pp[0].n[i0] = i; i = pp[0].x[j]; pp[0].x[j] =pp[0].x[i0]; pp[0].x[i0] = i; } for (j = 0, i1−−; j < i1; j++, i1−−) { i= pp[1].n[j]; pp[1].n[j] = pp[1].n[i1]; pp[1].n[i1] = i; i = pp[1].x[j];pp[1].x[j] = pp[1].x[i1]; pp[1].x[i1] = i; } if (fd >= 0) (void)close(fd); if (fj) { (void) unlink(jname); fj = 0; offset = 0; } } /*  *write a filled jmp struct offset of the prev one (if any): nw( )  */writejmps(ix) writejmps int ix; { char *mktemp( ); if (!fj) { if(mktemp(jname) < 0) { fprintf(stderr, “%s: can't mktemp( ) %s\n”, prog,jname); cleanup(1); } if ((fj = fopen(jname, “w”)) == 0) {fprintf(stderr, “%s: can't write %s\n”, prog, jname); exit(1); } }(void) fwrite((char *)&dx[ix].jp, sizeof(struct jmp), 1, fj); (void)fwrite((char *)&dx[ix].offset, sizeof(dx[ix].offset), 1, fj); }

TABLE 2 TAT XXXXXXXXXXXXXXX (Length = 15 amino acids) ComparisonXXXXXYYYYYYY (Length = 12 amino acids) Protein % amino acid sequenceidentity = (the number of identically matching amino acid residuesbetween the two polypeptide sequences as determined by ALIGN-2) dividedby (the total number of amino acid residues of the TAT polypeptide) = 5divided by 15 = 33.3%

TABLE 3 TAT XXXXXXXXXX (Length = 10 amino acids) ComparisonXXXXXYYYYYYZZYZ (Length = 15 amino acids) Protein % amino acid sequenceidentity = (the number of identically matching amino acid residuesbetween the two polypeptide sequences as determined by ALIGN-2) dividedby (the total number of amino acid residues of the TAT polypeptide) = 5divided by 10 = 50%

TABLE 4 TAT-DNA NNNNNNNNNNNNNN (Length = 14 nucleotides) ComparisonNNNNNNLLLLLLLLLL (Length = 16 nucleotides) DNA % nucleic acid sequenceidentity = (the number of identically matching nucleotides between thetwo nucleic acid sequences as determined by ALIGN-2) divided by (thetotal number of nucleotides of the TAT-DNA nucleic acid sequence) = 6divided by 14 = 42.9%

TABLE 5 TAT-DNA NNNNNNNNNNNN (Length = 12 nucleotides) Comparison DNANNNNLLLVV (Length = 9 nucleotides) % nucleic acid sequence identity =(the number of identically matching nucleotides between the two nucleicacid sequences as determined by ALIGN-2) divided by (the total number ofnucleotides of the TAT-DNA nucleic acid sequence) = 4 divided by 12 =33.3%

II. Compositions and Methods of the Invention

A. Anti-TAT Antibodies

In one embodiment, the present invention provides anti-TAT antibodieswhich may find use herein as therapeutic and/or diagnostic agents.Exemplary antibodies include polyclonal, monoclonal, humanized,bispecific, and heteroconjugate antibodies.

1. Polyclonal Antibodies

Polyclonal antibodies are preferably raised in animals by multiplesubcutaneous (sc) or intraperitoneal (ip) injections of the relevantantigen and an adjuvant. It may be useful to conjugate the relevantantigen (especially when synthetic peptides are used) to a protein thatis immunogenic in the species to be immunized. For example, the antigencan be conjugated to keyhole limpet hemocyanin (KLH), serum albumin,bovine thyroglobulin, or soybean trypsin inhibitor, using a bifunctionalor derivatizing agent, e.g., maleimidobenzoyl sulfosuccinimide ester(conjugation through cysteine residues), N-hydroxysuccinimide (throughlysine residues), glutaraldehyde, succinic anhydride, SOCl₂, orR¹N═C═NR, where R and R¹ are different alkyl groups.

Animals are immunized against the antigen, immunogenic conjugates, orderivatives by combining, e.g., 100 μg or 5 μg of the protein orconjugate (for rabbits or mice, respectively) with 3 volumes of Freund'scomplete adjuvant and injecting the solution intradermally at multiplesites. One month later, the animals are boosted with ⅕ to 1/10 theoriginal amount of peptide or conjugate in Freund's complete adjuvant bysubcutaneous injection at multiple sites. Seven to 14 days later, theanimals are bled and the serum is assayed for antibody titer. Animalsare boosted until the titer plateaus. Conjugates also can be made inrecombinant cell culture as protein fusions. Also, aggregating agentssuch as alum are suitably used to enhance the immune response.

2. Monoclonal Antibodies

Monoclonal antibodies may be made using the hybridoma method firstdescribed by Kohler et al., Nature, 256:495 (1975), or may be made byrecombinant DNA methods (U.S. Pat. No. 4,816,567).

In the hybridoma method, a mouse or other appropriate host animal, suchas a hamster, is immunized as described above to elicit lymphocytes thatproduce or are capable of producing antibodies that will specificallybind to the protein used for immunization. Alternatively, lymphocytesmay be immunized in vitro. After immunization, lymphocytes are isolatedand then fused with a myeloma cell line using a suitable fusing agent,such as polyethylene glycol, to form a hybridoma cell (Goding,Monoclonal Antibodies: Principles and Practice, pp. 59-103 (AcademicPress, 1986)).

The hybridoma cells thus prepared are seeded and grown in a suitableculture medium which medium preferably contains one or more substancesthat inhibit the growth or survival of the unfused, parental myelomacells (also referred to as fusion partner). For example, if the parentalmyeloma cells lack the enzyme hypoxanthine guanine phosphoribosyltransferase (HGPRT or HPRT), the selective culture medium for thehybridomas typically will include hypoxanthine, aminopterin, andthymidine (HAT medium), which substances prevent the growth ofHGPRT-deficient cells.

Preferred fusion partner myeloma cells are those that fuse efficiently,support stable high-level production of antibody by the selectedantibody-producing cells, and are sensitive to a selective medium thatselects against the unfused parental cells. Preferred myeloma cell linesare murine myeloma lines, such as those derived from MOPC-21 and MPC-11mouse tumors available from the Salk Institute Cell Distribution Center,San Diego, Calif. USA, and SP-2 and derivatives e.g., X63-Ag8-653 cellsavailable from the American Type Culture Collection, Manassas, Va., USA.Human myeloma and mouse-human heteromyeloma cell lines also have beendescribed for the production of human monoclonal antibodies (Kozbor, J.Immunol., 133:3001 (1984); and Brodeur et al., Monoclonal AntibodyProduction Techniques and Applications, pp. 51-63 (Marcel Dekker, Inc.,New York, 1987)).

Culture medium in which hybridoma cells are growing is assayed forproduction of monoclonal antibodies directed against the antigen.Preferably, the binding specificity of monoclonal antibodies produced byhybridoma cells is determined by immunoprecipitation or by an in vitrobinding assay, such as radioimmunoassay (RIA) or enzyme-linkedimmunosorbent assay (ELISA).

The binding affinity of the monoclonal antibody can, for example, bedetermined by the Scatchard analysis described in Munson et al., Anal.Biochem., 107:220 (1980).

Once hybridoma cells that produce antibodies of the desired specificity,affinity, and/or activity are identified, the clones may be subcloned bylimiting dilution procedures and grown by standard methods (Goding,Monoclonal Antibodies: Principles and Practice, pp. 59-103 (AcademicPress, 1986)). Suitable culture media for this purpose include, forexample, D-MEM or RPMI-1640 medium. In addition, the hybridoma cells maybe grown in vivo as ascites tumors in an animal e.g, by i.p. injectionof the cells into mice.

The monoclonal antibodies secreted by the subclones are suitablyseparated from the culture medium, ascites fluid, or serum byconventional antibody purification procedures such as, for example,affinity chromatography (e.g., using protein A or protein G-Sepharose)or ion-exchange chromatography, hydroxylapatite chromatography, gelelectrophoresis, dialysis, etc.

DNA encoding the monoclonal antibodies is readily isolated and sequencedusing conventional procedures (e.g., by using oligonucleotide probesthat are capable of binding specifically to genes encoding the heavy andlight chains of murine antibodies). The hybridoma cells serve as apreferred source of such DNA. Once isolated, the DNA may be placed intoexpression vectors, which are then transfected into host cells such asE. coli cells, simian COS cells, Chinese Hamster Ovary (CHO) cells, ormyeloma cells that do not otherwise produce antibody protein, to obtainthe synthesis of monoclonal antibodies in the recombinant host cells.Review articles on recombinant expression in bacteria of DNA encodingthe antibody include Skerra et al., Curr. Opinion in Immunol., 5:256-262(1993) and Plückthun, Immunol. Revs. 130:151-188 (1992).

In a further embodiment, monoclonal antibodies or antibody fragments canbe isolated from antibody phage libraries generated using the techniquesdescribed in McCafferty et al., Nature, 348:552-554 (1990). Clackson etal., Nature, 352:624-628 (1991) and Marks et al., J. Mol. Biol.,222:581-597 (1991) describe the isolation of murine and humanantibodies, respectively, using phage libraries. Subsequent publicationsdescribe the production of high affinity (nM range) human antibodies bychain shuffling (Marks et al., Bio/Technology, 10:779-783 (1992)), aswell as combinatorial infection and in vivo recombination as a strategyfor constructing very large phage libraries (Waterhouse et al., Nuc.Acids. Res. 21:2265-2266 (1993)). Thus, these techniques are viablealternatives to traditional monoclonal antibody hybridoma techniques forisolation of monoclonal antibodies.

The DNA that encodes the antibody may be modified to produce chimeric orfusion antibody polypeptides, for example, by substituting human heavychain and light chain constant domain (C_(H) and C_(L)) sequences forthe homologous murine sequences (U.S. Pat. No. 4,816,567; and Morrison,et al., Proc. Natl. Acad. Sci. USA, 81:6851 (1984)), or by fusing theimmunoglobulin coding sequence with all or part of the coding sequencefor a non-immunoglobulin polypeptide (heterologous polypeptide). Thenon-immunoglobulin polypeptide sequences can substitute for the constantdomains of an antibody, or they are substituted for the variable domainsof one antigen-combining site of an antibody to create a chimericbivalent antibody comprising one antigen-combining site havingspecificity for an antigen and another antigen-combining site havingspecificity for a different antigen.

3. Human and Humanized Antibodies

The anti-TAT antibodies of the invention may further comprise humanizedantibodies or human antibodies. Humanized forms of non-human (e.g.,murine) antibodies are chimeric immunoglobulins, immunoglobulin chainsor fragments thereof (such as Fv, Fab, Fab′, F(ab′)₂ or otherantigen-binding subsequences of antibodies) which contain minimalsequence derived from non-human immunoglobulin. Humanized antibodiesinclude human immunoglobulins (recipient antibody) in which residuesfrom a complementary determining region (CDR) of the recipient arereplaced by residues from a CDR of a non-human species (donor antibody)such as mouse, rat or rabbit having the desired specificity, affinityand capacity. In some instances, Fv framework residues of the humanimmunoglobulin are replaced by corresponding non-human residues.Humanized antibodies may also comprise residues which are found neitherin the recipient antibody nor in the imported CDR or frameworksequences. In general, the humanized antibody will comprisesubstantially all of at least one, and typically two, variable domains,in which all or substantially all of the CDR regions correspond to thoseof a non-human immunoglobulin and all or substantially all of the FRregions are those of a human immunoglobulin consensus sequence. Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region (Fc), typically that of a humanimmunoglobulin [Jones et al., Nature, 321:522-525 (1986); Riechmann etal., Nature, 332:323-329 (1988); and Presta, Curr. Op. Struct. Biol.,2:593-596 (1992)].

Methods for humanizing non-human antibodies are well known in the art.Generally, a humanized antibody has one or more amino acid residuesintroduced into it from a source which is non-human. These non-humanamino acid residues are often referred to as “import” residues, whichare typically taken from an “import” variable domain. Humanization canbe essentially performed following the method of Winter and co-workers[Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature,332:323-327 (1988); Verhoeyen et al., Science, 239:1534-1536 (1988)], bysubstituting rodent CDRs or CDR sequences for the correspondingsequences of a human antibody. Accordingly, such “humanized” antibodiesare chimeric antibodies (U.S. Pat. No. 4,816,567), wherein substantiallyless than an intact human variable domain has been substituted by thecorresponding sequence from a non-human species. In practice, humanizedantibodies are typically human antibodies in which some CDR residues andpossibly some FR residues are substituted by residues from analogoussites in rodent antibodies.

The choice of human variable domains, both light and heavy, to be usedin making the humanized antibodies is very important to reduceantigenicity and HAMA response (human anti-mouse antibody) when theantibody is intended for human therapeutic use. According to theso-called “best-fit” method, the sequence of the variable domain of arodent antibody is screened against the entire library of known humanvariable domain sequences. The human V domain sequence which is closestto that of the rodent is identified and the human framework region (FR)within it accepted for the humanized antibody (Sims et al., J. Immunol.151:2296 (1993); Chothia et al., J. Mol. Biol., 196:901 (1987)). Anothermethod uses a particular framework region derived from the consensussequence of all human antibodies of a particular subgroup of light orheavy chains. The same framework may be used for several differenthumanized antibodies (Carter et al., Proc. Natl. Acad. Sci. USA, 89:4285(1992); Presta et al., J. Immunol. 151:2623 (1993)).

It is further important that antibodies be humanized with retention ofhigh binding affinity for the antigen and other favorable biologicalproperties. To achieve this goal, according to a preferred method,humanized antibodies are prepared by a process of analysis of theparental sequences and various conceptual humanized products usingthree-dimensional models of the parental and humanized sequences.Three-dimensional immunoglobulin models are commonly available and arefamiliar to those skilled in the art. Computer programs are availablewhich illustrate and display probable three-dimensional conformationalstructures of selected candidate immunoglobulin sequences. Inspection ofthese displays permits analysis of the likely role of the residues inthe functioning of the candidate immunoglobulin sequence, i.e., theanalysis of residues that influence the ability of the candidateimmunoglobulin to bind its antigen. In this way, FR residues can beselected and combined from the recipient and import sequences so thatthe desired antibody characteristic, such as increased affinity for thetarget antigen(s), is achieved. In general, the hypervariable regionresidues are directly and most substantially involved in influencingantigen binding.

Various forms of a humanized anti-TAT antibody are contemplated. Forexample, the humanized antibody may be an antibody fragment, such as aFab, which is optionally conjugated with one or more cytotoxic agent(s)in order to generate an immunoconjugate. Alternatively, the humanizedantibody may be an intact antibody, such as an intact IgG1 antibody.

As an alternative to humanization, human antibodies can be generated.For example, it is now possible to produce transgenic animals (e.g.,mice) that are capable, upon immunization, of producing a fullrepertoire of human antibodies in the absence of endogenousimmunoglobulin production. For example, it has been described that thehomozygous deletion of the antibody heavy-chain joining region (J_(H))gene in chimeric and germ-line mutant mice results in completeinhibition of endogenous antibody production. Transfer of the humangerm-line immunoglobulin gene array into such germ-line mutant mice willresult in the production of human antibodies upon antigen challenge.See, e.g., Jakobovits et al., Proc. Natl. Acad. Sci. USA, 90:2551(1993); Jakobovits et al., Nature, 362:255-258 (1993); Bruggemann etal., Year in Immuno. 7:33 (1993); U.S. Pat. Nos. 5,545,806, 5,569,825,5,591,669 (all of GenPharm); 5,545,807; and WO 97/17852.

Alternatively, phage display technology (McCafferty et al., Nature348:552-553 [1990]) can be used to produce human antibodies and antibodyfragments in vitro, from immunoglobulin variable (V) domain generepertoires from unimmunized donors. According to this technique,antibody V domain genes are cloned in-frame into either a major or minorcoat protein gene of a filamentous bacteriophage, such as M13 or fd, anddisplayed as functional antibody fragments on the surface of the phageparticle. Because the filamentous particle contains a single-strandedDNA copy of the phage genome, selections based on the functionalproperties of the antibody also result in selection of the gene encodingthe antibody exhibiting those properties. Thus, the phage mimics some ofthe properties of the B-cell. Phage display can be performed in avariety of formats, reviewed in, e.g., Johnson, Kevin S, and Chiswell,David J., Current Opinion in Structural Biology, 3:564-571 (1993).Several sources of V-gene segments can be used for phage display.Clackson et al., Nature, 352:624-628 (1991) isolated a diverse array ofanti-oxazolone antibodies from a small random combinatorial library of Vgenes derived from the spleens of immunized mice. A repertoire of Vgenes from unimmunized human donors can be constructed and antibodies toa diverse array of antigens (including self-antigens) can be isolatedessentially following the techniques described by Marks et al., J. Mol.Biol. 222:581-597 (1991), or Griffith et al., EMBO J. 12:725-734 (1993).See, also, U.S. Pat. Nos. 5,565,332 and 5,573,905.

As discussed above, human antibodies may also be generated by in vitroactivated B cells (see U.S. Pat. Nos. 5,567,610 and 5,229,275).

4. Antibody Fragments

In certain circumstances there are advantages of using antibodyfragments, rather than whole antibodies. The smaller size of thefragments allows for rapid clearance, and may lead to improved access tosolid tumors.

Various techniques have been developed for the production of antibodyfragments. Traditionally, these fragments were derived via proteolyticdigestion of intact antibodies (see, e.g., Morimoto et al., Journal ofBiochemical and Biophysical Methods 24:107-117 (1992); and Brennan etal., Science, 229:81 (1985)). However, these fragments can now beproduced directly by recombinant host cells. Fab, Fv and ScFv antibodyfragments can all be expressed in and secreted from E. coli, thusallowing the facile production of large amounts of these fragments.Antibody fragments can be isolated from the antibody phage librariesdiscussed above. Alternatively, Fab′-SH fragments can be directlyrecovered from E. coli and chemically coupled to form F(ab′)₂ fragments(Carter et al., Bio/Technology 10:163-167 (1992)). According to anotherapproach, F(ab′)₂ fragments can be isolated directly from recombinanthost cell culture. Fab and F(ab′)₂ fragment with increased in vivohalf-life comprising a salvage receptor binding epitope residues aredescribed in U.S. Pat. No. 5,869,046. Other techniques for theproduction of antibody fragments will be apparent to the skilledpractitioner. In other embodiments, the antibody of choice is a singlechain Fv fragment (scFv). See WO 93/16185; U.S. Pat. No. 5,571,894; andU.S. Pat. No. 5,587,458. Fv and sFv are the only species with intactcombining sites that are devoid of constant regions; thus, they aresuitable for reduced nonspecific binding during in vivo use. sFv fusionproteins may be constructed to yield fusion of an effector protein ateither the amino or the carboxy terminus of an sFv. See AntibodyEngineering, ed. Borrebaeck, supra. The antibody fragment may also be a“linear antibody”, e.g., as described in U.S. Pat. No. 5,641,870 forexample. Such linear antibody fragments may be monospecific orbispecific.

5. Bispecific Antibodies

Bispecific antibodies are antibodies that have binding specificities forat least two different epitopes. Exemplary bispecific antibodies maybind to two different epitopes of a TAT protein as described herein.Other such antibodies may combine a TAT binding site with a binding sitefor another protein. Alternatively, an anti-TAT arm may be combined withan arm which binds to a triggering molecule on a leukocyte such as aT-cell receptor molecule (e.g. CD3), or Fc receptors for IgG (FcγR),such as FcγRI (CD64), FcγRII (CD32) and FcγRIII (CD16), so as to focusand localize cellular defense mechanisms to the TAT-expressing cell.Bispecific antibodies may also be used to localize cytotoxic agents tocells which express TAT. These antibodies possess a TAT-binding arm andan arm which binds the cytotoxic agent (e.g., saporin,anti-interferon-α, vinca alkaloid, ricin A chain, methotrexate orradioactive isotope hapten). Bispecific antibodies can be prepared asfull length antibodies or antibody fragments (e.g., F(ab′)₂ bispecificantibodies).

WO 96/16673 describes a bispecific anti-ErbB2/anti-FcγRIII antibody andU.S. Pat. No. 5,837,234 discloses a bispecific anti-ErbB2/anti-FcγRIantibody. A bispecific anti-ErbB2/Fcα antibody is shown in WO98/02463.U.S. Pat. No. 5,821,337 teaches a bispecific anti-ErbB2/anti-CD3antibody.

Methods for making bispecific antibodies are known in the art.Traditional production of full length bispecific antibodies is based onthe co-expression of two immunoglobulin heavy chain-light chain pairs,where the two chains have different specificities (Millstein et al.,Nature 305:537-539 (1983)). Because of the random assortment ofimmunoglobulin heavy and light chains, these hybridomas (quadromas)produce a potential mixture of 10 different antibody molecules, of whichonly one has the correct bispecific structure. Purification of thecorrect molecule, which is usually done by affinity chromatographysteps, is rather cumbersome, and the product yields are low. Similarprocedures are disclosed in WO 93/08829, and in Traunecker et al., EMBOJ. 10:3655-3659 (1991).

According to a different approach, antibody variable domains with thedesired binding specificities (antibody-antigen combining sites) arefused to immunoglobulin constant domain sequences. Preferably, thefusion is with an Ig heavy chain constant domain, comprising at leastpart of the hinge, C_(H)2, and C_(H)3 regions. It is preferred to havethe first heavy-chain constant region (C_(H)1) containing the sitenecessary for light chain bonding, present in at least one of thefusions. DNAs encoding the immunoglobulin heavy chain fusions and, ifdesired, the immunoglobulin light chain, are inserted into separateexpression vectors, and are co-transfected into a suitable host cell.This provides for greater flexibility in adjusting the mutualproportions of the three polypeptide fragments in embodiments whenunequal ratios of the three polypeptide chains used in the constructionprovide the optimum yield of the desired bispecific antibody. It is,however, possible to insert the coding sequences for two or all threepolypeptide chains into a single expression vector when the expressionof at least two polypeptide chains in equal ratios results in highyields or when the ratios have no significant affect on the yield of thedesired chain combination.

In a preferred embodiment of this approach, the bispecific antibodiesare composed of a hybrid immunoglobulin heavy chain with a first bindingspecificity in one arm, and a hybrid immunoglobulin heavy chain-lightchain pair (providing a second binding specificity) in the other arm. Itwas found that this asymmetric structure facilitates the separation ofthe desired bispecific compound from unwanted immunoglobulin chaincombinations, as the presence of an immunoglobulin light chain in onlyone half of the bispecific molecule provides for a facile way ofseparation. This approach is disclosed in WO 94/04690. For furtherdetails of generating bispecific antibodies see, for example, Suresh etal., Methods in Enzymology 121:210 (1986).

According to another approach described in U.S. Pat. No. 5,731,168, theinterface between a pair of antibody molecules can be engineered tomaximize the percentage of heterodimers which are recovered fromrecombinant cell culture. The preferred interface comprises at least apart of the C_(H)3 domain. In this method, one or more small amino acidside chains from the interface of the first antibody molecule arereplaced with larger side chains (e.g., tyrosine or tryptophan).Compensatory “cavities” of identical or similar size to the large sidechain(s) are created on the interface of the second antibody molecule byreplacing large amino acid side chains with smaller ones (e.g., alanineor threonine). This provides a mechanism for increasing the yield of theheterodimer over other unwanted end-products such as homodimers.

Bispecific antibodies include cross-linked or “heteroconjugate”antibodies. For example, one of the antibodies in the heteroconjugatecan be coupled to avidin, the other to biotin. Such antibodies have, forexample, been proposed to target immune system cells to unwanted cells(U.S. Pat. No. 4,676,980), and for treatment of HIV infection (WO91/00360, WO 92/200373, and EP 03089). Heteroconjugate antibodies may bemade using any convenient cross-linking methods. Suitable cross-linkingagents are well known in the art, and are disclosed in U.S. Pat. No.4,676,980, along with a number of cross-linking techniques.

Techniques for generating bispecific antibodies from antibody fragmentshave also been described in the literature. For example, bispecificantibodies can be prepared using chemical linkage. Brennan et al.,Science 229:81 (1985) describe a procedure wherein intact antibodies areproteolytically cleaved to generate F(ab′)₂ fragments. These fragmentsare reduced in the presence of the dithiol complexing agent, sodiumarsenite, to stabilize vicinal dithiols and prevent intermoleculardisulfide formation. The Fab′ fragments generated are then converted tothionitrobenzoate (TNB) derivatives. One of the Fab′-TNB derivatives isthen reconverted to the Fab′-thiol by reduction with mercaptoethylamineand is mixed with an equimolar amount of the other Fab′-TNB derivativeto form the bispecific antibody. The bispecific antibodies produced canbe used as agents for the selective immobilization of enzymes.

Recent progress has facilitated the direct recovery of Fab′-SH fragmentsfrom E. coli, which can be chemically coupled to form bispecificantibodies. Shalaby et al., J. Exp. Med. 175: 217-225 (1992) describethe production of a fully humanized bispecific antibody F(ab′)₂molecule. Each Fab′ fragment was separately secreted from E. coli andsubjected to directed chemical coupling in vitro to form the bispecificantibody. The bispecific antibody thus formed was able to bind to cellsoverexpressing the ErbB2 receptor and normal human T cells, as well astrigger the lytic activity of human cytotoxic lymphocytes against humanbreast tumor targets. Various techniques for making and isolatingbispecific antibody fragments directly from recombinant cell culturehave also been described. For example, bispecific antibodies have beenproduced using leucine zippers. Kostelny et al., J. Immunol.148(5):1547-1553 (1992). The leucine zipper peptides from the Fos andJun proteins were linked to the Fab′ portions of two differentantibodies by gene fusion. The antibody homodimers were reduced at thehinge region to form monomers and then re-oxidized to form the antibodyheterodimers. This method can also be utilized for the production ofantibody homodimers. The “diabody” technology described by Hollinger etal., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993) has provided analternative mechanism for making bispecific antibody fragments. Thefragments comprise a V_(H) connected to a V_(L) by a linker which is tooshort to allow pairing between the two domains on the same chain.Accordingly, the V_(H) and V_(L) domains of one fragment are forced topair with the complementary V_(L) and V_(H) domains of another fragment,thereby forming two antigen-binding sites. Another strategy for makingbispecific antibody fragments by the use of single-chain Fv (sFv) dimershas also been reported. See Gruber et al., J. Immunol., 152:5368 (1994).

Antibodies with more than two valencies are contemplated. For example,trispecific antibodies can be prepared. Tutt et al., J. Immunol. 147:60(1991).

6. Heteroconjugate Antibodies

Heteroconjugate antibodies are also within the scope of the presentinvention. Heteroconjugate antibodies are composed of two covalentlyjoined antibodies. Such antibodies have, for example, been proposed totarget immune system cells to unwanted cells [U.S. Pat. No. 4,676,980],and for treatment of HIV infection [WO 91/00360; WO 92/200373; EP03089]. It is contemplated that the antibodies may be prepared in vitrousing known methods in synthetic protein chemistry, including thoseinvolving crosslinking agents. For example, immunotoxins may beconstructed using a disulfide exchange reaction or by forming athioether bond. Examples of suitable reagents for this purpose includeiminothiolate and methyl-4-mercaptobutyrimidate and those disclosed, forexample, in U.S. Pat. No. 4,676,980.

7. Multivalent Antibodies

A multivalent antibody may be internalized (and/or catabolized) fasterthan a bivalent antibody by a cell expressing an antigen to which theantibodies bind. The antibodies of the present invention can bemultivalent antibodies (which are other than of the IgM class) withthree or more antigen binding sites (e.g. tetravalent antibodies), whichcan be readily produced by recombinant expression of nucleic acidencoding the polypeptide chains of the antibody. The multivalentantibody can comprise a dimerization domain and three or more antigenbinding sites. The preferred dimerization domain comprises (or consistsof) an Fc region or a hinge region. In this scenario, the antibody willcomprise an Fc region and three or more antigen binding sitesamino-terminal to the Fc region. The preferred multivalent antibodyherein comprises (or consists of) three to about eight, but preferablyfour, antigen binding sites. The multivalent antibody comprises at leastone polypeptide chain (and preferably two polypeptide chains), whereinthe polypeptide chain(s) comprise two or more variable domains. Forinstance, the polypeptide chain(s) may compriseVD1-(X1)_(n)-VD2-(X2)_(n)-Fc, wherein VD1 is a first variable domain,VD2 is a second variable domain, Fc is one polypeptide chain of an Fcregion, X1 and X2 represent an amino acid or polypeptide, and n is 0or 1. For instance, the polypeptide chain(s) may comprise:VH-CH1-flexible linker-VH-CH1-Fc region chain; or VH-CH1-VH-CH1-Fcregion chain. The multivalent antibody herein preferably furthercomprises at least two (and preferably four) light chain variable domainpolypeptides. The multivalent antibody herein may, for instance,comprise from about two to about eight light chain variable domainpolypeptides. The light chain variable domain polypeptides contemplatedhere comprise a light chain variable domain and, optionally, furthercomprise a CL domain.

8. Effector Function Engineering

It may be desirable to modify the antibody of the invention with respectto effector function, e.g., so as to enhance antigen-dependentcell-mediated cyotoxicity (ADCC) and/or complement dependentcytotoxicity (CDC) of the antibody. This may be achieved by introducingone or more amino acid substitutions in an Fc region of the antibody.Alternatively or additionally, cysteine residue(s) may be introduced inthe Fc region, thereby allowing interchain disulfide bond formation inthis region. The homodimeric antibody thus generated may have improvedinternalization capability and/or increased complement-mediated cellkilling and antibody-dependent cellular cytotoxicity (ADCC). See Caronet al., J. Exp Med. 176:1191-1195 (1992) and Shopes, B. J. Immunol.148:2918-2922 (1992). Homodimeric antibodies with enhanced anti-tumoractivity may also be prepared using heterobifunctional cross-linkers asdescribed in Wolff et al., Cancer Research 53:2560-2565 (1993).Alternatively, an antibody can be engineered which has dual Fc regionsand may thereby have enhanced complement lysis and ADCC capabilities.See Stevenson et al., Anti-Cancer Drug Design 3:219-230 (1989). Toincrease the serum half life of the antibody, one may incorporate asalvage receptor binding epitope into the antibody (especially anantibody fragment) as described in U.S. Pat. No. 5,739,277, for example.As used herein, the term “salvage receptor binding epitope” refers to anepitope of the Fc region of an IgG molecule (e.g., IgG₁, IgG₂, IgG₃, orIgG₄) that is responsible for increasing the in vivo serum half-life ofthe IgG molecule.

9. Immunoconjugates

The invention also pertains to immunoconjugates comprising an antibodyconjugated to a cytotoxic agent such as a chemotherapeutic agent, agrowth inhibitory agent, a toxin (e.g., an enzymatically active toxin ofbacterial, fungal, plant, or animal origin, or fragments thereof), or aradioactive isotope (i.e., a radioconjugate).

Chemotherapeutic agents useful in the generation of suchimmunoconjugates have been described above. Enzymatically active toxinsand fragments thereof that can be used include diphtheria A chain,nonbinding active fragments of diphtheria toxin, exotoxin A chain (fromPseudomonas aeruginosa), ricin A chain, abrin A chain, modeccin A chain,alpha-sarcin, Aleurites fordii proteins, dianthin proteins, Phytolacaamericana proteins (PAPI, PAPII, and PAP-S), momordica charantiainhibitor, curcin, crotin, sapaonaria officinalis inhibitor, gelonin,mitogellin, restrictocin, phenomycin, enomycin, and the tricothecenes. Avariety of radionuclides are available for the production ofradioconjugated antibodies. Examples include ²¹²Bi, ¹³¹I, ¹³¹In, ⁹⁰Y,and ¹⁸⁶Re. Conjugates of the antibody and cytotoxic agent are made usinga variety of bifunctional protein-coupling agents such asN-succinimidyl-3-(2-pyridyldithiol) propionate (SPDP), iminothiolane(IT), bifunctional derivatives of imidoesters (such as dimethyladipimidate HCL), active esters (such as disuccinimidyl suberate),aldehydes (such as glutareldehyde), bis-azido compounds (such asbis(p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (such asbis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science, 238: 1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026.

Conjugates of an antibody and one or more small molecule toxins, such asa calicheamicin, maytansinoids, a trichothene, and CC1065, and thederivatives of these toxins that have toxin activity, are alsocontemplated herein.

Maytansine and Maytansinoids

In one preferred embodiment, an anti-TAT antibody (full length orfragments) of the invention is conjugated to one or more maytansinoidmolecules.

Maytansinoids are mitototic inhibitors which act by inhibiting tubulinpolymerization. Maytansine was first isolated from the east Africanshrub Maytenus serrata (U.S. Pat. No. 3,896,111). Subsequently, it wasdiscovered that certain microbes also produce maytansinoids, such asmaytansinol and C-3 maytansinol esters (U.S. Pat. No. 4,151,042).Synthetic maytansinol and derivatives and analogues thereof aredisclosed, for example, in U.S. Pat. Nos. 4,137,230; 4,248,870;4,256,746; 4,260,608; 4,265,814; 4,294,757; 4,307,016; 4,308,268;4,308,269; 4,309,428; 4,313,946; 4,315,929; 4,317,821; 4,322,348;4,331,598; 4,361,650; 4,364,866; 4,424,219; 4,450,254; 4,362,663; and4,371,533, the disclosures of which are hereby expressly incorporated byreference.

Maytansinoid-Antibody Conjugates

In an attempt to improve their therapeutic index, maytansine andmaytansinoids have been conjugated to antibodies specifically binding totumor cell antigens. Immunoconjugates containing maytansinoids and theirtherapeutic use are disclosed, for example, in U.S. Pat. Nos. 5,208,020,5,416,064 and European Patent EP 0 425 235 B1, the disclosures of whichare hereby expressly incorporated by reference. Liu et al., Proc. Natl.Acad. Sci. USA 93:8618-8623 (1996) described immunoconjugates comprisinga maytansinoid designated DM1 linked to the monoclonal antibody C242directed against human colorectal cancer. The conjugate was found to behighly cytotoxic towards cultured colon cancer cells, and showedantitumor activity in an in vivo tumor growth assay. Chari et al.,Cancer Research 52:127-131 (1992) describe immunoconjugates in which amaytansinoid was conjugated via a disulfide linker to the murineantibody A7 binding to an antigen on human colon cancer cell lines, orto another murine monoclonal antibody TA.1 that binds the HER-2/neuoncogene. The cytotoxicity of the TA.1-maytansonoid conjugate was testedin vitro on the human breast cancer cell line SK-BR-3, which expresses3×10⁵ HER-2 surface antigens per cell. The drug conjugate achieved adegree of cytotoxicity similar to the free maytansonid drug, which couldbe increased by increasing the number of maytansinoid molecules perantibody molecule. The A7-maytansinoid conjugate showed low systemiccytotoxicity in mice.

Anti-Tat Polypeptide Antibody-Maytansinoid Conjugates (Immunoconjugates)

Anti-TAT antibody-maytansinoid conjugates are prepared by chemicallylinking an anti-TAT antibody to a maytansinoid molecule withoutsignificantly diminishing the biological activity of either the antibodyor the maytansinoid molecule. An average of 3-4 maytansinoid moleculesconjugated per antibody molecule has shown efficacy in enhancingcytotoxicity of target cells without negatively affecting the functionor solubility of the antibody, although even one molecule oftoxin/antibody would be expected to enhance cytotoxicity over the use ofnaked antibody. Maytansinoids are well known in the art and can besynthesized by known techniques or isolated from natural sources.Suitable maytansinoids are disclosed, for example, in U.S. Pat. No.5,208,020 and in the other patents and nonpatent publications referredto hereinabove. Preferred maytansinoids are maytansinol and maytansinolanalogues modified in the aromatic ring or at other positions of themaytansinol molecule, such as various maytansinol esters.

There are many linking groups known in the art for makingantibody-maytansinoid conjugates, including, for example, thosedisclosed in U.S. Pat. No. 5,208,020 or EP Patent 0 425 235 B1, andChari et al., Cancer Research 52:127-131 (1992). The linking groupsinclude disufide groups, thioether groups, acid labile groups,photolabile groups, peptidase labile groups, or esterase labile groups,as disclosed in the above-identified patents, disulfide and thioethergroups being preferred.

Conjugates of the antibody and maytansinoid may be made using a varietyof bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate,iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCL), active esters (such as disuccinimidylsuberate), aldehydes (such as glutareldehyde), bis-azido compounds (suchas bis(p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astoluene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). Particularly preferred coupling agentsinclude N-succinimidyl-3-(2-pyridyldithio) propionate (SPDP) (Carlssonet al., Biochem. J. 173:723-737 [1978]) andN-succinimidyl-4-(2-pyridylthio)pentanoate (SPP) to provide for adisulfide linkage.

The linker may be attached to the maytansinoid molecule at variouspositions, depending on the type of the link. For example, an esterlinkage may be formed by reaction with a hydroxyl group usingconventional coupling techniques. The reaction may occur at the C-3position having a hydroxyl group, the C-14 position modified withhyrdoxymethyl, the C-15 position modified with a hydroxyl group, and theC-20 position having a hydroxyl group. In a preferred embodiment, thelinkage is formed at the C-3 position of maytansinol or a maytansinolanalogue.

Calicheamicin

Another immunoconjugate of interest comprises an anti-TAT antibodyconjugated to one or more calicheamicin molecules. The calicheamicinfamily of antibiotics are capable of producing double-stranded DNAbreaks at sub-picomolar concentrations. For the preparation ofconjugates of the calicheamicin family, see U.S. Pat. Nos. 5,712,374,5,714,586, 5,739,116, 5,767,285, 5,770,701, 5,770,710, 5,773,001,5,877,296 (all to American Cyanamid Company). Structural analogues ofcalicheamicin which may be used include, but are not limited to, γ₁^(I), α₂ ^(I), α₃ ^(I), N-acetyl-γ₁ ^(I), PSAG and θ^(I) ₁ (Hinman etal., Cancer Research 53:3336-3342 (1993), Lode et al., Cancer Research58:2925-2928 (1998) and the aforementioned U.S. patents to AmericanCyanamid). Another anti-tumor drug that the antibody can be conjugatedis QFA which is an antifolate. Both calicheamicin and QFA haveintracellular sites of action and do not readily cross the plasmamembrane. Therefore, cellular uptake of these agents through antibodymediated internalization greatly enhances their cytotoxic effects.

Other Cytotoxic Agents

Other antitumor agents that can be conjugated to the anti-TAT antibodiesof the invention include BCNU, streptozoicin, vincristine and5-fluorouracil, the family of agents known collectively LL-E33288complex described in U.S. Pat. Nos. 5,053,394, 5,770,710, as well asesperamicins (U.S. Pat. No. 5,877,296).

Enzymatically active toxins and fragments thereof which can be usedinclude diphtheria A chain, nonbinding active fragments of diphtheriatoxin, exotoxin A chain (from Pseudomonas aeruginosa), ricin A chain,abrin A chain, modeccin A chain, alpha-sarcin, Aleurites fordiiproteins, dianthin proteins, Phytolaca americana proteins (PAPI, PAPII,and PAP-S), momordica charantia inhibitor, curcin, crotin, sapaonariaofficinalis inhibitor, gelonin, mitogellin, restrictocin, phenomycin,enomycin and the tricothecenes. See, for example, WO 93/21232 publishedOct. 28, 1993.

The present invention further contemplates an immunoconjugate formedbetween an antibody and a compound with nucleolytic activity (e.g., aribonuclease or a DNA endonuclease such as a deoxyribonuclease; DNase).

For selective destruction of the tumor, the antibody may comprise ahighly radioactive atom. A variety of radioactive isotopes are availablefor the production of radioconjugated anti-TAT antibodies. Examplesinclude At²¹¹, I¹³¹, I¹²⁵, Y⁹⁰, Re¹⁸⁶, Re¹⁸⁸, Sm¹⁵³, Bi²¹², P³², Pb²¹²and radioactive isotopes of Lu. When the conjugate is used fordiagnosis, it may comprise a radioactive atom for scintigraphic studies,for example tc^(99m) or I¹²³, or a spin label for nuclear magneticresonance (NMR) imaging (also known as magnetic resonance imaging, mri),such as iodine-123 again, iodine-131, indium-111, fluorine-19,carbon-13, nitrogen-15, oxygen-17, gadolinium, manganese or iron.

The radio- or other labels may be incorporated in the conjugate in knownways. For example, the peptide may be biosynthesized or may besynthesized by chemical amino acid synthesis using suitable amino acidprecursors involving, for example, fluorine-19 in place of hydrogen.Labels such as tc^(99m) or I¹²³, Re¹⁸⁶, Re¹⁸⁸ and In¹¹¹ can be attachedvia a cysteine residue in the peptide. Yttrium-90 can be attached via alysine residue. The IODOGEN method (Fraker et al (1978) Biochem.Biophys. Res. Commun. 80: 49-57 can be used to incorporate iodine-123.“Monoclonal Antibodies in Immunoscintigraphy” (Chatal, CRC Press 1989)describes other methods in detail.

Conjugates of the antibody and cytotoxic agent may be made using avariety of bifunctional protein coupling agents such asN-succinimidyl-3-(2-pyridyldithio) propionate (SPDP),succinimidyl-4-(N-maleimidomethyl)cyclohexane-1-carboxylate,iminothiolane (IT), bifunctional derivatives of imidoesters (such asdimethyl adipimidate HCL), active esters (such as disuccinimidylsuberate), aldehydes (such as glutareldehyde), bis-azido compounds (suchas bis(p-azidobenzoyl) hexanediamine), bis-diazonium derivatives (suchas bis-(p-diazoniumbenzoyl)-ethylenediamine), diisocyanates (such astolyene 2,6-diisocyanate), and bis-active fluorine compounds (such as1,5-difluoro-2,4-dinitrobenzene). For example, a ricin immunotoxin canbe prepared as described in Vitetta et al., Science 238:1098 (1987).Carbon-14-labeled 1-isothiocyanatobenzyl-3-methyldiethylenetriaminepentaacetic acid (MX-DTPA) is an exemplary chelating agent forconjugation of radionucleotide to the antibody. See WO94/11026. Thelinker may be a “cleavable linker” facilitating release of the cytotoxicdrug in the cell. For example, an acid-labile linker,peptidase-sensitive linker, photolabile linker, dimethyl linker ordisulfide-containing linker (Chari et al., Cancer Research 52:127-131(1992); U.S. Pat. No. 5,208,020) may be used.

Alternatively, a fusion protein comprising the anti-TAT antibody andcytotoxic agent may be made, e.g., by recombinant techniques or peptidesynthesis. The length of DNA may comprise respective regions encodingthe two portions of the conjugate either adjacent one another orseparated by a region encoding a linker peptide which does not destroythe desired properties of the conjugate.

In yet another embodiment, the antibody may be conjugated to a“receptor” (such streptavidin) for utilization in tumor pre-targetingwherein the antibody-receptor conjugate is administered to the patient,followed by removal of unbound conjugate from the circulation using aclearing agent and then administration of a “ligand” (e.g., avidin)which is conjugated to a cytotoxic agent (e.g., a radionucleotide).

10. Immunoliposomes

The anti-TAT antibodies disclosed herein may also be formulated asimmunoliposomes. A “liposome” is a small vesicle composed of varioustypes of lipids, phospholipids and/or surfactant which is useful fordelivery of a drug to a mammal. The components of the liposome arecommonly arranged in a bilayer formation, similar to the lipidarrangement of biological membranes. Liposomes containing the antibodyare prepared by methods known in the art, such as described in Epsteinet al., Proc. Natl. Acad. Sci. USA 82:3688 (1985); Hwang et al., Proc.Natl. Acad. Sci. USA 77:4030 (1980); U.S. Pat. Nos. 4,485,045 and4,544,545; and WO97/38731 published Oct. 23, 1997. Liposomes withenhanced circulation time are disclosed in U.S. Pat. No. 5,013,556.

Particularly useful liposomes can be generated by the reverse phaseevaporation method with a lipid composition comprisingphosphatidylcholine, cholesterol and PEG-derivatizedphosphatidylethanolamine (PEG-PE). Liposomes are extruded throughfilters of defined pore size to yield liposomes with the desireddiameter. Fab′ fragments of the antibody of the present invention can beconjugated to the liposomes as described in Martin et al., J. Biol.Chem. 257:286-288 (1982) via a disulfide interchange reaction. Achemotherapeutic agent is optionally contained within the liposome. SeeGabizon et al., J. National Cancer Inst. 81(19):1484 (1989).

B. TAT Binding Oligopeptides

TAT binding oligopeptides of the present invention are oligopeptidesthat bind, preferably specifically, to a TAT polypeptide as describedherein. TAT binding oligopeptides may be chemically synthesized usingknown oligopeptide synthesis methodology or may be prepared and purifiedusing recombinant technology. TAT binding oligopeptides are usually atleast about 5 amino acids in length, alternatively at least about 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79,80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97,98, 99, or 100 amino acids in length or more, wherein such oligopeptidesthat are capable of binding, preferably specifically, to a TATpolypeptide as described herein. TAT binding oligopeptides may beidentified without undue experimentation using well known techniques. Inthis regard, it is noted that techniques for screening oligopeptidelibraries for oligopeptides that are capable of specifically binding toa polypeptide target are well known in the art (see, e.g., U.S. Pat.Nos. 5,556,762, 5,750,373, 4,708,871, 4,833,092, 5,223,409, 5,403,484,5,571,689, 5,663,143; PCT Publication Nos. WO 84/03506 and WO84/03564;Geysen et al., Proc. Natl. Acad. Sci. U.S.A., 81:3998-4002 (1984);Geysen et al., Proc. Natl. Acad. Sci. U.S.A., 82:178-182 (1985); Geysenet al., in Synthetic Peptides as Antigens, 130-149 (1986); Geysen etal., J. Immunol. Meth., 102:259-274 (1987); Schoofs et al., J. Immunol.,140:611-616 (1988), Cwirla, S. E. et al. (1990) Proc. Natl. Acad. Sci.USA, 87:6378; Lowman, H. B. et al. (1991) Biochemistry, 30:10832;Clackson, T. et al. (1991) Nature, 352: 624; Marks, J. D. et al. (1991),J. Mol. Biol., 222:581; Kang, A. S. et al. (1991) Proc. Natl. Acad. Sci.USA, 88:8363, and Smith, G. P. (1991) Current Opin. Biotechnol., 2:668).

In this regard, bacteriophage (phage) display is one well knowntechnique which allows one to screen large oligopeptide libraries toidentify member(s) of those libraries which are capable of specificallybinding to a polypeptide target. Phage display is a technique by whichvariant polypeptides are displayed as fusion proteins to the coatprotein on the surface of bacteriophage particles (Scott, J. K. andSmith, G. P. (1990) Science 249: 386). The utility of phage display liesin the fact that large libraries of selectively randomized proteinvariants (or randomly cloned cDNAs) can be rapidly and efficientlysorted for those sequences that bind to a target molecule with highaffinity. Display of peptide (Cwirla, S. E. et al. (1990) Proc. Natl.Acad. Sci. USA, 87:6378) or protein (Lowman, H. B. et al. (1991)Biochemistry, 30:10832; Clackson, T. et al. (1991) Nature, 352: 624;Marks, J. D. et al. (1991), J. Mol. Biol., 222:581; Kang, A. S. et al.(1991) Proc. Natl. Acad. Sci. USA, 88:8363) libraries on phage have beenused for screening millions of polypeptides or oligopeptides for oneswith specific binding properties (Smith, G. P. (1991) Current Opin.Biotechnol., 2:668). Sorting phage libraries of random mutants requiresa strategy for constructing and propagating a large number of variants,a procedure for affinity purification using the target receptor, and ameans of evaluating the results of binding enrichments. U.S. Pat. Nos.5,223,409, 5,403,484, 5,571,689, and 5,663,143.

Although most phage display methods have used filamentous phage;lambdoid phage display systems (WO 95/34683; U.S. Pat. No. 5,627,024),T4 phage display systems (Ren, Z-J. et al. (1998) Gene 215:439; Zhu, Z.(1997) CAN 33:534; Jiang, J. et al. (1997) can 128:44380; Ren, Z-J. etal. (1997) CAN 127:215644; Ren, Z-J. (1996) Protein Sci. 5:1833; Efimov,V. P. et al. (1995) Virus Genes 10:173) and T7 phage display systems(Smith, G. P. and Scott, J. K. (1993) Methods in Enzymology, 217,228_(—)257; U.S. Pat. No. 5,766,905) are also known.

Many other improvements and variations of the basic phage displayconcept have now been developed. These improvements enhance the abilityof display systems to screen peptide libraries for binding to selectedtarget molecules and to display functional proteins with the potentialof screening these proteins for desired properties. Combinatorialreaction devices for phage display reactions have been developed (WO98/14277) and phage display libraries have been used to analyze andcontrol bimolecular interactions (WO 98/20169; WO 98/20159) andproperties of constrained helical peptides (WO 98/20036). WO 97/35196describes a method of isolating an affinity ligand in which a phagedisplay library is contacted with one solution in which the ligand willbind to a target molecule and a second solution in which the affinityligand will not bind to the target molecule, to selectively isolatebinding ligands. WO 97/46251 describes a method of biopanning a randomphage display library with an affinity purified antibody and thenisolating binding phage, followed by a micropanning process usingmicroplate wells to isolate high affinity binding phage. The use ofStaphlylococcus aureus protein A as an affinity tag has also beenreported (Li et al. (1998) Mol. Biotech., 9:187). WO 97/47314 describesthe use of substrate subtraction libraries to distinguish enzymespecificities using a combinatorial library which may be a phage displaylibrary. A method for selecting enzymes suitable for use in detergentsusing phage display is described in WO 97/09446. Additional methods ofselecting specific binding proteins are described in U.S. Pat. Nos.5,498,538, 5,432,018, and WO 98/15833.

Methods of generating peptide libraries and screening these librariesare also disclosed in U.S. Pat. Nos. 5,723,286, 5,432,018, 5,580,717,5,427,908, 5,498,530, 5,770,434, 5,734,018, 5,698,426, 5,763,192, and5,723,323.

C. TAT Binding Organic Molecules

TAT binding organic molecules are organic molecules other thanoligopeptides or antibodies as defined herein that bind, preferablyspecifically, to a TAT polypeptide as described herein. TAT bindingorganic molecules may be identified and chemically synthesized usingknown methodology (see, e.g., PCT Publication Nos. WO00/00823 andWO00/39585). TAT binding organic molecules are usually less than about2000 daltons in size, alternatively less than about 1500, 750, 500, 250or 200 daltons in size, wherein such organic molecules that are capableof binding, preferably specifically, to a TAT polypeptide as describedherein may be identified without undue experimentation using well knowntechniques. In this regard, it is noted that techniques for screeningorganic molecule libraries for molecules that are capable of binding toa polypeptide target are well known in the art (see, e.g., PCTPublication Nos. WO00/00823 and WO00/39585). TAT binding organicmolecules may be, for example, aldehydes, ketones, oximes, hydrazones,semicarbazones, carbazides, primary amines, secondary amines, tertiaryamines, N-substituted hydrazines, hydrazides, alcohols, ethers, thiols,thioethers, disulfides, carboxylic acids, esters, amides, ureas,carbamates, carbonates, ketals, thioketals, acetals, thioacetals, arylhalides, aryl sulfonates, alkyl halides, alkyl sulfonates, aromaticcompounds, heterocyclic compounds, anilines, alkenes, alkynes, diols,amino alcohols, oxazolidines, oxazolines, thiazolidines, thiazolines,enamines, sulfonamides, epoxides, aziridines, isocyanates, sulfonylchlorides, diazo compounds, acid chlorides, or the like.

D. Screening for Anti-TAT Antibodies, TAT Binding Oligopeptides and TATBinding Organic Molecules With the Desired Properties

Techniques for generating antibodies, oligopeptides and organicmolecules that bind to TAT polypeptides have been described above. Onemay further select antibodies, oligopeptides or other organic moleculeswith certain biological characteristics, as desired.

The growth inhibitory effects of an anti-TAT antibody, oligopeptide orother organic molecule of the invention may be assessed by methods knownin the art, e.g., using cells which express a TAT polypeptide eitherendogenously or following transfection with the TAT gene. For example,appropriate tumor cell lines and TAT-transfected cells may treated withan anti-TAT monoclonal antibody, oligopeptide or other organic moleculeof the invention at various concentrations for a few days (e.g., 2-7)days and stained with crystal violet or MTT or analyzed by some othercolorimetric assay. Another method of measuring proliferation would beby comparing ³H-thymidine uptake by the cells treated in the presence orabsence an anti-TAT antibody, TAT binding oligopeptide or TAT bindingorganic molecule of the invention. After treatment, the cells areharvested and the amount of radioactivity incorporated into the DNAquantitated in a scintillation counter. Appropriate positive controlsinclude treatment of a selected cell line with a growth inhibitoryantibody known to inhibit growth of that cell line. Growth inhibition oftumor cells in vivo can be determined in various ways known in the art.Preferably, the tumor cell is one that overexpresses a TAT polypeptide.Preferably, the anti-TAT antibody, TAT binding oligopeptide or TATbinding organic molecule will inhibit cell proliferation of aTAT-expressing tumor cell in vitro or in vivo by about 25-100% comparedto the untreated tumor cell, more preferably, by about 30-100%, and evenmore preferably by about 50-100% or 70-100%, in one embodiment, at anantibody concentration of about 0.5 to 30 g/ml. Growth inhibition can bemeasured at an antibody concentration of about 0.5 to 30 μg/ml or about0.5 nM to 200 nM in cell culture, where the growth inhibition isdetermined 1-10 days after exposure of the tumor cells to the antibody.The antibody is growth inhibitory in vivo if administration of theanti-TAT antibody at about 1 μg/kg to about 100 mg/kg body weightresults in reduction in tumor size or reduction of tumor cellproliferation within about 5 days to 3 months from the firstadministration of the antibody, preferably within about 5 to 30 days.

To select for an anti-TAT antibody, TAT binding oligopeptide or TATbinding organic molecule which induces cell death, loss of membraneintegrity as indicated by, e.g., propidium iodide (PI), trypan blue or7AAD uptake may be assessed relative to control. A PI uptake assay canbe performed in the absence of complement and immune effector cells. TATpolypeptide-expressing tumor cells are incubated with medium alone ormedium containing the appropriate anti-TAT antibody (e.g, at aboutμg/ml), TAT binding oligopeptide or TAT binding organic molecule. Thecells are incubated for a 3 day time period. Following each treatment,cells are washed and aliquoted into 35 mm strainer-capped 12×75 tubes (1ml per tube, 3 tubes per treatment group) for removal of cell clumps.Tubes then receive PI (10 μg/ml). Samples may be analyzed using aFACSCAN® flow cytometer and FACSCONVERT® CellQuest software (BectonDickinson). Those anti-TAT antibodies, TAT binding oligopeptides or TATbinding organic molecules that induce statistically significant levelsof cell death as determined by PI uptake may be selected as celldeath-inducing anti-TAT antibodies, TAT binding oligopeptides or TATbinding organic molecules.

To screen for antibodies, oligopeptides or other organic molecules whichbind to an epitope on a TAT polypeptide bound by an antibody ofinterest, a routine cross-blocking assay such as that described inAntibodies, A Laboratory Manual, Cold Spring Harbor Laboratory, EdHarlow and David Lane (1988), can be performed. This assay can be usedto determine if a test antibody, oligopeptide or other organic moleculebinds the same site or epitope as a known anti-TAT antibody.Alternatively, or additionally, epitope mapping can be performed bymethods known in the art. For example, the antibody sequence can bemutagenized such as by alanine scanning, to identify contact residues.The mutant antibody is initially tested for binding with polyclonalantibody to ensure proper folding. In a different method, peptidescorresponding to different regions of a TAT polypeptide can be used incompetition assays with the test antibodies or with a test antibody andan antibody with a characterized or known epitope.

E. Antibody Dependent Enzyme Mediated Prodrug Therapy (ADEPT)

The antibodies of the present invention may also be used in ADEPT byconjugating the antibody to a prodrug-activating enzyme which converts aprodrug (e.g., a peptidyl chemotherapeutic agent, see WO81/01145) to anactive anti-cancer drug. See, for example, WO 88/07378 and U.S. Pat. No.4,975,278.

The enzyme component of the immunoconjugate useful for ADEPT includesany enzyme capable of acting on a prodrug in such a way so as to covertit into its more active, cytotoxic form.

Enzymes that are useful in the method of this invention include, but arenot limited to, alkaline phosphatase useful for convertingphosphate-containing prodrugs into free drugs; arylsulfatase useful forconverting sulfate-containing prodrugs into free drugs; cytosinedeaminase useful for converting non-toxic 5-fluorocytosine into theanti-cancer drug, 5-fluorouracil; proteases, such as serratia protease,thermolysin, subtilisin, carboxypeptidases and cathepsins (such ascathepsins B and L), that are useful for converting peptide-containingprodrugs into free drugs; D-alanylcarboxypeptidases, useful forconverting prodrugs that contain D-amino acid substituents;carbohydrate-cleaving enzymes such as β-galactosidase and neuraminidaseuseful for converting glycosylated prodrugs into free drugs; β-lactamaseuseful for converting drugs derivatized with β-lactams into free drugs;and penicillin amidases, such as penicillin V amidase or penicillin Gamidase, useful for converting drugs derivatized at their aminenitrogens with phenoxyacetyl or phenylacetyl groups, respectively, intofree drugs. Alternatively, antibodies with enzymatic activity, alsoknown in the art as “abzymes”, can be used to convert the prodrugs ofthe invention into free active drugs (see, e.g., Massey, Nature328:457-458 (1987)). Antibody-abzyme conjugates can be prepared asdescribed herein for delivery of the abzyme to a tumor cell population.

The enzymes of this invention can be covalently bound to the anti-TATantibodies by techniques well known in the art such as the use of theheterobifunctional crosslinking reagents discussed above. Alternatively,fusion proteins comprising at least the antigen binding region of anantibody of the invention linked to at least a functionally activeportion of an enzyme of the invention can be constructed usingrecombinant DNA techniques well known in the art (see, e.g., Neubergeret al., Nature 312:604-608 (1984).

F. Full-Length TAT Polypeptides

The present invention also provides newly identified and isolatednucleotide sequences encoding polypeptides referred to in the presentapplication as TAT polypeptides. In particular, cDNAs (partial andfull-length) encoding various TAT polypeptides have been identified andisolated, as disclosed in further detail in the Examples below.

As disclosed in the Examples below, various cDNA clones have beendeposited with the ATCC. The actual nucleotide sequences of those clonescan readily be determined by the skilled artisan by sequencing of thedeposited clone using routine methods in the art. The predicted aminoacid sequence can be determined from the nucleotide sequence usingroutine skill. For the TAT polypeptides and encoding nucleic acidsdescribed herein, in some cases, Applicants have identified what isbelieved to be the reading frame best identifiable with the sequenceinformation available at the time.

G. Anti-TAT Antibody and TAT Polypeptide Variants

In addition to the anti-TAT antibodies and full-length native sequenceTAT polypeptides described herein, it is contemplated that anti-TATantibody and TAT polypeptide variants can be prepared. Anti-TAT antibodyand TAT polypeptide variants can be prepared by introducing appropriatenucleotide changes into the encoding DNA, and/or by synthesis of thedesired antibody or polypeptide. Those skilled in the art willappreciate that amino acid changes may alter post-translationalprocesses of the anti-TAT antibody or TAT polypeptide, such as changingthe number or position of glycosylation sites or altering the membraneanchoring characteristics.

Variations in the anti-TAT antibodies and TAT polypeptides describedherein, can be made, for example, using any of the techniques andguidelines for conservative and non-conservative mutations set forth,for instance, in U.S. Pat. No. 5,364,934. Variations may be asubstitution, deletion or insertion of one or more codons encoding theantibody or polypeptide that results in a change in the amino acidsequence as compared with the native sequence antibody or polypeptide.Optionally the variation is by substitution of at least one amino acidwith any other amino acid in one or more of the domains of the anti-TATantibody or TAT polypeptide. Guidance in determining which amino acidresidue may be inserted, substituted or deleted without adverselyaffecting the desired activity may be found by comparing the sequence ofthe anti-TAT antibody or TAT polypeptide with that of homologous knownprotein molecules and minimizing the number of amino acid sequencechanges made in regions of high homology. Amino acid substitutions canbe the result of replacing one amino acid with another amino acid havingsimilar structural and/or chemical properties, such as the replacementof a leucine with a serine, i.e., conservative amino acid replacements.Insertions or deletions may optionally be in the range of about 1 to 5amino acids. The variation allowed may be determined by systematicallymaking insertions, deletions or substitutions of amino acids in thesequence and testing the resulting variants for activity exhibited bythe full-length or mature native sequence.

Anti-TAT antibody and TAT polypeptide fragments are provided herein.Such fragments may be truncated at the N-terminus or C-terminus, or maylack internal residues, for example, when compared with a full lengthnative antibody or protein. Certain fragments lack amino acid residuesthat are not essential for a desired biological activity of the anti-TATantibody or TAT polypeptide.

Anti-TAT antibody and TAT polypeptide fragments may be prepared by anyof a number of conventional techniques. Desired peptide fragments may bechemically synthesized. An alternative approach involves generatingantibody or polypeptide fragments by enzymatic digestion, e.g., bytreating the protein with an enzyme known to cleave proteins at sitesdefined by particular amino acid residues, or by digesting the DNA withsuitable restriction enzymes and isolating the desired fragment. Yetanother suitable technique involves isolating and amplifying a DNAfragment encoding a desired antibody or polypeptide fragment, bypolymerase chain reaction (PCR). Oligonucleotides that define thedesired termini of the DNA fragment are employed at the 5′ and 3′primers in the PCR. Preferably, anti-TAT antibody and TAT polypeptidefragments share at least one biological and/or immunological activitywith the native anti-TAT antibody or TAT polypeptide disclosed herein.

In particular embodiments, conservative substitutions of interest areshown in Table 6 under the heading of preferred substitutions. If suchsubstitutions result in a change in biological activity, then moresubstantial changes, denominated exemplary substitutions in Table 6, oras further described below in reference to amino acid classes, areintroduced and the products screened.

TABLE 6 Original Exemplary Preferred Residue Substitutions SubstitutionsAla (A) val; leu; ile val Arg (R) lys; gln; asn lys Asn (N) gln; his;lys; arg gln Asp (D) glu glu Cys (C) ser ser Gln (Q) asn asn Glu (E) aspasp Gly (G) pro; ala ala His (H) asn; gln; lys; arg arg Ile (I) leu;val; met; ala; phe; leu norleucine Leu (L) norleucine; ile; val; ilemet; ala; phe Lys (K) arg; gln; asn arg Met (M) leu; phe; ile leu Phe(F) leu; val; ile; ala; tyr leu Pro (P) ala ala Ser (S) thr thr Thr (T)ser ser Trp (W) tyr; phe tyr Tyr (Y) trp; phe; thr; ser phe Val (V) ile;leu; met; phe; leu ala; norleucine

Substantial modifications in function or immunological identity of theanti-TAT antibody or TAT polypeptide are accomplished by selectingsubstitutions that differ significantly in their effect on maintaining(a) the structure of the polypeptide backbone in the area of thesubstitution, for example, as a sheet or helical conformation, (b) thecharge or hydrophobicity of the molecule at the target site, or (c) thebulk of the side chain. Naturally occurring residues are divided intogroups based on common side-chain properties:

(1) hydrophobic: norleucine, met, ala, val, leu, ile;(2) neutral hydrophilic: cys, ser, thr;(3) acidic: asp, glu;(4) basic: asn, gln, his, lys, arg;(5) residues that influence chain orientation: gly, pro; and(6) aromatic: trp, tyr, phe.

Non-conservative substitutions will entail exchanging a member of one ofthese classes for another class. Such substituted residues also may beintroduced into the conservative substitution sites or, more preferably,into the remaining (non-conserved) sites.

The variations can be made using methods known in the art such asoligonucleotide-mediated (site-directed) mutagenesis, alanine scanning,and PCR mutagenesis. Site-directed mutagenesis [Carter et al., Nucl.Acids Res., 13:4331 (1986); Zoller et al., Nucl. Acids Res., 10:6487(1987)], cassette mutagenesis [Wells et al., Gene, 34:315 (1985)],restriction selection mutagenesis [Wells et al., Philos. Trans. R. Soc.London SerA, 317:415 (1986)] or other known techniques can be performedon the cloned DNA to produce the anti-TAT antibody or TAT polypeptidevariant DNA.

Scanning amino acid analysis can also be employed to identify one ormore amino acids along a contiguous sequence. Among the preferredscanning amino acids are relatively small, neutral amino acids. Suchamino acids include alanine, glycine, serine, and cysteine. Alanine istypically a preferred scanning amino acid among this group because iteliminates the side-chain beyond the beta-carbon and is less likely toalter the main-chain conformation of the variant [Cunningham and Wells,Science, 244:1081-1085 (1989)]. Alanine is also typically preferredbecause it is the most common amino acid. Further, it is frequentlyfound in both buried and exposed positions [Creighton, The Proteins,(W.H. Freeman & Co., N.Y.); Chothia, J. Mol. Biol., 150:1 (1976)]. Ifalanine substitution does not yield adequate amounts of variant, anisoteric amino acid can be used.

Any cysteine residue not involved in maintaining the proper conformationof the anti-TAT antibody or TAT polypeptide also may be substituted,generally with serine, to improve the oxidative stability of themolecule and prevent aberrant crosslinking. Conversely, cysteine bond(s)may be added to the anti-TAT antibody or TAT polypeptide to improve itsstability (particularly where the antibody is an antibody fragment suchas an Fv fragment).

A particularly preferred type of substitutional variant involvessubstituting one or more hypervariable region residues of a parentantibody (e.g., a humanized or human antibody). Generally, the resultingvariant(s) selected for further development will have improvedbiological properties relative to the parent antibody from which theyare generated. A convenient way for generating such substitutionalvariants involves affinity maturation using phage display. Briefly,several hypervariable region sites (e.g., 6-7 sites) are mutated togenerate all possible amino substitutions at each site. The antibodyvariants thus generated are displayed in a monovalent fashion fromfilamentous phage particles as fusions to the gene III product of M13packaged within each particle. The phage-displayed variants are thenscreened for their biological activity (e.g., binding affinity) asherein disclosed. In order to identify candidate hypervariable regionsites for modification, alanine scanning mutagenesis can be performed toidentify hypervariable region residues contributing significantly toantigen binding. Alternatively, or additionally, it may be beneficial toanalyze a crystal structure of the antigen-antibody complex to identifycontact points between the antibody and human TAT polypeptide. Suchcontact residues and neighboring residues are candidates forsubstitution according to the techniques elaborated herein. Once suchvariants are generated, the panel of variants is subjected to screeningas described herein and antibodies with superior properties in one ormore relevant assays may be selected for further development.

Nucleic acid molecules encoding amino acid sequence variants of theanti-TAT antibody are prepared by a variety of methods known in the art.These methods include, but are not limited to, isolation from a naturalsource (in the case of naturally occurring amino acid sequence variants)or preparation by oligonucleotide-mediated (or site-directed)mutagenesis, PCR mutagenesis, and cassette mutagenesis of an earlierprepared variant or a non-variant version of the anti-TAT antibody.

H. Modifications of Anti-TAT Antibodies and TAT Polypeptides

Covalent modifications of anti-TAT antibodies and TAT polypeptides areincluded within the scope of this invention. One type of covalentmodification includes reacting targeted amino acid residues of ananti-TAT antibody or TAT polypeptide with an organic derivatizing agentthat is capable of reacting with selected side chains or the N- orC-terminal residues of the anti-TAT antibody or TAT polypeptide.Derivatization with bifunctional agents is useful, for instance, forcrosslinking anti-TAT antibody or TAT polypeptide to a water-insolublesupport matrix or surface for use in the method for purifying anti-TATantibodies, and vice-versa. Commonly used crosslinking agents include,e.g., 1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylicacid, homobifunctional imidoesters, including disuccinimidyl esters suchas 3,3′-dithiobis(succinimidylpropionate), bifunctional maleimides suchas bis-N-maleimido-1,8-octane and agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate.

Other modifications include deamidation of glutaminyl and asparaginylresidues to the corresponding glutamyl and aspartyl residues,respectively, hydroxylation of proline and lysine, phosphorylation ofhydroxyl groups of seryl or threonyl residues, methylation of theα-amino groups of lysine, arginine, and histidine side chains [T. E.Creighton, Proteins: Structure and Molecular Properties, W.H. Freeman &Co., San Francisco, pp. 79-86 (1983)], acetylation of the N-terminalamine, and amidation of any C-terminal carboxyl group.

Another type of covalent modification of the anti-TAT antibody or TATpolypeptide included within the scope of this invention comprisesaltering the native glycosylation pattern of the antibody orpolypeptide. “Altering the native glycosylation pattern” is intended forpurposes herein to mean deleting one or more carbohydrate moieties foundin native sequence anti-TAT antibody or TAT polypeptide (either byremoving the underlying glycosylation site or by deleting theglycosylation by chemical and/or enzymatic means), and/or adding one ormore glycosylation sites that are not present in the native sequenceanti-TAT antibody or TAT polypeptide. In addition, the phrase includesqualitative changes in the glycosylation of the native proteins,involving a change in the nature and proportions of the variouscarbohydrate moieties present.

Glycosylation of antibodies and other polypeptides is typically eitherN-linked or O-linked. N-linked refers to the attachment of thecarbohydrate moiety to the side chain of an asparagine residue. Thetripeptide sequences asparagine-X-serine and asparagine-X-threonine,where X is any amino acid except proline, are the recognition sequencesfor enzymatic attachment of the carbohydrate moiety to the asparagineside chain. Thus, the presence of either of these tripeptide sequencesin a polypeptide creates a potential glycosylation site. O-linkedglycosylation refers to the attachment of one of the sugarsN-aceylgalactosamine, galactose, or xylose to a hydroxyamino acid, mostcommonly serine or threonine, although 5-hydroxyproline or5-hydroxylysine may also be used.

Addition of glycosylation sites to the anti-TAT antibody or TATpolypeptide is conveniently accomplished by altering the amino acidsequence such that it contains one or more of the above-describedtripeptide sequences (for N-linked glycosylation sites). The alterationmay also be made by the addition of, or substitution by, one or moreserine or threonine residues to the sequence of the original anti-TATantibody or TAT polypeptide (for O-linked glycosylation sites). Theanti-TAT antibody or TAT polypeptide amino acid sequence may optionallybe altered through changes at the DNA level, particularly by mutatingthe DNA encoding the anti-TAT antibody or TAT polypeptide at preselectedbases such that codons are generated that will translate into thedesired amino acids.

Another means of increasing the number of carbohydrate moieties on theanti-TAT antibody or TAT polypeptide is by chemical or enzymaticcoupling of glycosides to the polypeptide. Such methods are described inthe art, e.g., in WO 87/05330 published 11 Sep. 1987, and in Aplin andWriston, CRC Crit. Rev. Biochem., pp. 259-306 (1981).

Removal of carbohydrate moieties present on the anti-TAT antibody or TATpolypeptide may be accomplished chemically or enzymatically or bymutational substitution of codons encoding for amino acid residues thatserve as targets for glycosylation. Chemical deglycosylation techniquesare known in the art and described, for instance, by Hakimuddin, et al.,Arch. Biochem. Biophys., 259:52 (1987) and by Edge et al., Anal.Biochem., 118:131 (1981). Enzymatic cleavage of carbohydrate moieties onpolypeptides can be achieved by the use of a variety of endo- andexo-glycosidases as described by Thotakura et al., Meth. Enzymol.,138:350 (1987).

Another type of covalent modification of anti-TAT antibody or TATpolypeptide comprises linking the antibody or polypeptide to one of avariety of nonproteinaceous polymers, e.g., polyethylene glycol (PEG),polypropylene glycol, or polyoxyalkylenes, in the manner set forth inU.S. Pat. No. 4,640,835; 4,496,689; 4,301,144; 4,670,417; 4,791,192 or4,179,337. The antibody or polypeptide also may be entrapped inmicrocapsules prepared, for example, by coacervation techniques or byinterfacial polymerization (for example, hydroxymethylcellulose orgelatin-microcapsules and poly-(methylmethacylate) microcapsules,respectively), in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules), or in macroemulsions. Such techniques are disclosed inRemington's Pharmaceutical Sciences, 16th edition, Oslo, A., Ed.,(1980).

The anti-TAT antibody or TAT polypeptide of the present invention mayalso be modified in a way to form chimeric molecules comprising ananti-TAT antibody or TAT polypeptide fused to another, heterologouspolypeptide or amino acid sequence.

In one embodiment, such a chimeric molecule comprises a fusion of theanti-TAT antibody or TAT polypeptide with a tag polypeptide whichprovides an epitope to which an anti-tag antibody can selectively bind.The epitope tag is generally placed at the amino- or carboxyl-terminusof the anti-TAT antibody or TAT polypeptide. The presence of suchepitope-tagged forms of the anti-TAT antibody or TAT polypeptide can bedetected using an antibody against the tag polypeptide. Also, provisionof the epitope tag enables the anti-TAT antibody or TAT polypeptide tobe readily purified by affinity purification using an anti-tag antibodyor another type of affinity matrix that binds to the epitope tag.Various tag polypeptides and their respective antibodies are well knownin the art. Examples include poly-histidine (poly-his) orpoly-histidine-glycine (poly-his-gly) tags; the flu HA tag polypeptideand its antibody 12CA5 [Field et al., Mol. Cell. Biol., 8:2159-2165(1988)]; the c-myc tag and the 8F9, 3C7, 6E10, G4, B7 and 9E10antibodies thereto [Evan et al., Molecular and Cellular Biology,5:3610-3616 (1985)]; and the Herpes Simplex virus glycoprotein D (gD)tag and its antibody [Paborsky et al., Protein Engineering, 3(6):547-553(1990)]. Other tag polypeptides include the Flag-peptide [Hopp et al.,BioTechnology, 6:1204-1210 (1988)]; the KT3 epitope peptide [Martin etal., Science, 255:192-194 (1992)]; an α-tubulin epitope peptide [Skinneret al., J. Biol. Chem., 266:15163-15166 (1991)]; and the T7 gene 10protein peptide tag [Lutz-Freyermuth et al., Proc. Natl. Acad. Sci. USA,87:6393-6397 (1990)].

In an alternative embodiment, the chimeric molecule may comprise afusion of the anti-TAT antibody or TAT polypeptide with animmunoglobulin or a particular region of an immunoglobulin. For abivalent form of the chimeric molecule (also referred to as an“immunoadhesin”), such a fusion could be to the Fc region of an IgGmolecule. The Ig fusions preferably include the substitution of asoluble (transmembrane domain deleted or inactivated) form of ananti-TAT antibody or TAT polypeptide in place of at least one variableregion within an Ig molecule. In a particularly preferred embodiment,the immunoglobulin fusion includes the hinge, CH₂ and CH₃, or the hinge,CH₁, CH₂ and CH₃ regions of an IgG 1 molecule. For the production ofimmunoglobulin fusions see also U.S. Pat. No. 5,428,130 issued Jun. 27,1995.

I. Preparation of Anti-TAT Antibodies and TAT Polypeptides

The description below relates primarily to production of anti-TATantibodies and TAT polypeptides by culturing cells transformed ortransfected with a vector containing anti-TAT antibody- and TATpolypeptide-encoding nucleic acid. It is, of course, contemplated thatalternative methods, which are well known in the art, may be employed toprepare anti-TAT antibodies and TAT polypeptides. For instance, theappropriate amino acid sequence, or portions thereof, may be produced bydirect peptide synthesis using solid-phase techniques [see, e.g.,Stewart et al., Solid-Phase Peptide Synthesis, W.H. Freeman Co., SanFrancisco, Calif. (1969); Merrifield, J. Am. Chem. Soc., 85:2149-2154(1963)]. In vitro protein synthesis may be performed using manualtechniques or by automation. Automated synthesis may be accomplished,for instance, using an Applied Biosystems Peptide Synthesizer (FosterCity, Calif.) using manufacturer's instructions. Various portions of theanti-TAT antibody or TAT polypeptide may be chemically synthesizedseparately and combined using chemical or enzymatic methods to producethe desired anti-TAT antibody or TAT polypeptide.

1. Isolation of DNA Encoding Anti-TAT Antibody or TAT Polypeptide

DNA encoding anti-TAT antibody or TAT polypeptide may be obtained from acDNA library prepared from tissue believed to possess the anti-TATantibody or TAT polypeptide mRNA and to express it at a detectablelevel. Accordingly, human anti-TAT antibody or TAT polypeptide DNA canbe conveniently obtained from a cDNA library prepared from human tissue.The anti-TAT antibody- or TAT polypeptide-encoding gene may also beobtained from a genomic library or by known synthetic procedures (e.g.,automated nucleic acid synthesis).

Libraries can be screened with probes (such as oligonucleotides of atleast about 20-80 bases) designed to identify the gene of interest orthe protein encoded by it. Screening the cDNA or genomic library withthe selected probe may be conducted using standard procedures, such asdescribed in Sambrook et al., Molecular Cloning: A Laboratory Manual(New York: Cold Spring Harbor Laboratory Press, 1989). An alternativemeans to isolate the gene encoding anti-TAT antibody or TAT polypeptideis to use PCR methodology [Sambrook et al., supra; Dieffenbach et al.,PCR Primer: A Laboratory Manual (Cold Spring Harbor Laboratory Press,1995)].

Techniques for screening a cDNA library are well known in the art. Theoligonucleotide sequences selected as probes should be of sufficientlength and sufficiently unambiguous that false positives are minimized.The oligonucleotide is preferably labeled such that it can be detectedupon hybridization to DNA in the library being screened. Methods oflabeling are well known in the art, and include the use of radiolabelslike ³²P-labeled ATP, biotinylation or enzyme labeling. Hybridizationconditions, including moderate stringency and high stringency, areprovided in Sambrook et al., supra.

Sequences identified in such library screening methods can be comparedand aligned to other known sequences deposited and available in publicdatabases such as GenBank or other private sequence databases. Sequenceidentity (at either the amino acid or nucleotide level) within definedregions of the molecule or across the full-length sequence can bedetermined using methods known in the art and as described herein.

Nucleic acid having protein coding sequence may be obtained by screeningselected cDNA or genomic libraries using the deduced amino acid sequencedisclosed herein for the first time, and, if necessary, usingconventional primer extension procedures as described in Sambrook etal., supra, to detect precursors and processing intermediates of mRNAthat may not have been reverse-transcribed into cDNA.

2. Selection and Transformation of Host Cells

Host cells are transfected or transformed with expression or cloningvectors described herein for anti-TAT antibody or TAT polypeptideproduction and cultured in conventional nutrient media modified asappropriate for inducing promoters, selecting transformants, oramplifying the genes encoding the desired sequences. The cultureconditions, such as media, temperature, pH and the like, can be selectedby the skilled artisan without undue experimentation. In general,principles, protocols, and practical techniques for maximizing theproductivity of cell cultures can be found in Mammalian CellBiotechnology: a Practical Approach, M. Butler, ed. (IRL Press, 1991)and Sambrook et al., supra.

Methods of eukaryotic cell transfection and prokaryotic celltransformation are known to the ordinarily skilled artisan, for example,CaCl₂, CaPO₄, liposome-mediated and electroporation. Depending on thehost cell used, transformation is performed using standard techniquesappropriate to such cells. The calcium treatment employing calciumchloride, as described in Sambrook et al., supra, or electroporation isgenerally used for prokaryotes. Infection with Agrobacterium tumefaciensis used for transformation of certain plant cells, as described by Shawet al., Gene, 23:315 (1983) and WO 89/05859 published 29 Jun. 1989. Formammalian cells without such cell walls, the calcium phosphateprecipitation method of Graham and van der Eb, Virology, 52:456-457(1978) can be employed. General aspects of mammalian cell host systemtransfections have been described in U.S. Pat. No. 4,399,216.Transformations into yeast are typically carried out according to themethod of Van Solingen et al., J. Bact., 130:946 (1977) and Hsiao etal., Proc. Natl. Acad. Sci. (USA), 76:3829 (1979). However, othermethods for introducing DNA into cells, such as by nuclearmicroinjection, electroporation, bacterial protoplast fusion with intactcells, or polycations, e.g., polybrene, polyornithine, may also be used.For various techniques for transforming mammalian cells, see Keown etal., Methods in Enzymology, 185:527-537 (1990) and Mansour et al.,Nature, 336:348-352 (1988).

Suitable host cells for cloning or expressing the DNA in the vectorsherein include prokaryote, yeast, or higher eukaryote cells. Suitableprokaryotes include but are not limited to eubacteria, such asGram-negative or Gram-positive organisms, for example,Enterobacteriaceae such as E. coli. Various E. coli strains are publiclyavailable, such as E. coli K12 strain MM294 (ATCC 31,446); E. coli X1776(ATCC 31,537); E. coli strain W3110 (ATCC 27,325) and K5 772 (ATCC53,635). Other suitable prokaryotic host cells includeEnterobacteriaceae such as Escherichia, e.g., E. coli, Enterobacter,Erwinia, Klebsiella, Proteus, Salmonella, e.g., Salmonella typhimurium,Serratia, e.g., Serratia marcescans, and Shigella, as well as Bacillisuch as B. subtilis and B. licheniformis (e.g., B. licheniformis 41Pdisclosed in DD 266,710 published 12 Apr. 1989), Pseudomonas such as P.aeruginosa, and Streptomyces. These examples are illustrative ratherthan limiting. Strain W3110 is one particularly preferred host or parenthost because it is a common host strain for recombinant DNA productfermentations. Preferably, the host cell secretes minimal amounts ofproteolytic enzymes. For example, strain W3110 may be modified to effecta genetic mutation in the genes encoding proteins endogenous to thehost, with examples of such hosts including E. coli W3110 strain 1 A2,which has the complete genotype tonA; E. coli W3110 strain 9E4, whichhas the complete genotype tonA ptr3; E. coli W3110 strain 27C7 (ATCC55,244), which has the complete genotype tonA ptr3 phoA E15 (argF-lac)169 degP ompT kan^(r) ; E. coli W3110 strain 37D6, which has thecomplete genotype tonA ptr3 phoA E15 (argF-lac) 169 degP ompT rbs7 ilvGkan^(r) ; E. coli W3110 strain 40B4, which is strain 37D6 with anon-kanamycin resistant degP deletion mutation; and an E. coli strainhaving mutant periplasmic protease disclosed in U.S. Pat. No. 4,946,783issued 7 Aug. 1990. Alternatively, in vitro methods of cloning, e.g.,PCR or other nucleic acid polymerase reactions, are suitable.

Full length antibody, antibody fragments, and antibody fusion proteinscan be produced in bacteria, in particular when glycosylation and Fceffector function are not needed, such as when the therapeutic antibodyis conjugated to a cytotoxic agent (e.g., a toxin) and theimmunoconjugate by itself shows effectiveness in tumor cell destruction.Full length antibodies have greater half life in circulation. Productionin E. coli is faster and more cost efficient. For expression of antibodyfragments and polypeptides in bacteria, see, e.g., U.S. Pat. No.5,648,237 (Carter et. al.), U.S. Pat. No. 5,789,199 (Joly et al.), andU.S. Pat. No. 5,840,523 (Simmons et al.) which describes translationinitiation regio (TIR) and signal sequences for optimizing expressionand secretion, these patents incorporated herein by reference. Afterexpression, the antibody is isolated from the E. coli cell paste in asoluble fraction and can be purified through, e.g., a protein A or Gcolumn depending on the isotype. Final purification can be carried outsimilar to the process for purifying antibody expressed e.g, in CHOcells.

In addition to prokaryotes, eukaryotic microbes such as filamentousfungi or yeast are suitable cloning or expression hosts for anti-TATantibody- or TAT polypeptide-encoding vectors. Saccharomyces cerevisiaeis a commonly used lower eukaryotic host microorganism. Others includeSchizosaccharomyces pombe (Beach and Nurse, Nature, 290:140 [1981]; EP139,383 published 2 May 1985); Kluyveromyces hosts (U.S. Pat. No.4,943,529; Fleer et al., Bio/Technology, 9:968-975 (1991)) such as,e.g., K. lactis (MW98-8C, CBS683, CBS4574; Louvencourt et al., J.Bacteriol., 154(2):737-742 [1983]), K. fragilis (ATCC 12,424), K.bulgaricus (ATCC 16,045), K. wickeramii (ATCC 24,178), K. waltii (ATCC56,500), K. drosophilarum (ATCC 36,906; Van den Berg et al.,Bio/Technology, 8:135 (1990)), K. thermotolerans, and K. marxianus;yarrowia (EP 402,226); Pichia pastoris (EP 183,070; Sreekrishna et al.,J. Basic Microbiol., 28:265-278 [1988]); Candida, Trichoderma reesia (EP244,234); Neurospora crassa (Case et al., Proc. Natl. Acad. Sci. USA,76:5259-5263 [1979]); Schwanniomyces such as Schwanniomyces occidentalis(EP 394,538 published 31 Oct. 1990); and filamentous fungi such as,e.g., Neurospora, Penicillium, Tolypocladium (WO 91/00357 published 10Jan. 1991), and Aspergillus hosts such as A. nidulans (Ballance et al.,Biochem. Biophvs. Res. Commun., 112:284-289 [1983]; Tilburn et al.,Gene, 26:205-221 [1983]; Yelton et al., Proc. Natl. Acad. Sci. USA, 81:1470-1474 [1984]) and A. niger (Kelly and Hynes, EMBO J., 4:475-479[1985]). Methylotropic yeasts are suitable herein and include, but arenot limited to, yeast capable of growth on methanol selected from thegenera consisting of Hansenula, Candida, Kloeckera, Pichia,Saccharomyces, Torulopsis, and Rhodotorula. A list of specific speciesthat are exemplary of this class of yeasts may be found in C. Anthony,The Biochemistry of Methylotrophs, 269 (1982).

Suitable host cells for the expression of glycosylated anti-TAT antibodyor TAT polypeptide are derived from multicellular organisms. Examples ofinvertebrate cells include insect cells such as Drosophila S2 andSpodoptera Sf9, as well as plant cells, such as cell cultures of cotton,corn, potato, soybean, petunia, tomato, and tobacco. Numerousbaculoviral strains and variants and corresponding permissive insecthost cells from hosts such as Spodoptera frugiperda (caterpillar), Aedesaegypti (mosquito), Aedes albopictus (mosquito), Drosophila melanogaster(fruitfly), and Bombyx mori have been identified. A variety of viralstrains for transfection are publicly available, e.g., the L-1 variantof Autographa californica NPV and the Bm-5 strain of Bombyx mori NPV,and such viruses may be used as the virus herein according to thepresent invention, particularly for transfection of Spodopterafrugiperda cells.

However, interest has been greatest in vertebrate cells, and propagationof vertebrate cells in culture (tissue culture) has become a routineprocedure. Examples of useful mammalian host cell lines are monkeykidney CV1 line transformed by SV40 (COS-7, ATCC CRL 1651); humanembryonic kidney line (293 or 293 cells subcloned for growth insuspension culture, Graham et al., J. Gen Virol. 36:59 (1977)); babyhamster kidney cells (BHK, ATCC CCL 10); Chinese hamster ovarycells/−DHFR(CHO, Urlaub et al., Proc. Natl. Acad. Sci. USA 77:4216(1980)); mouse sertoli cells (TM4, Mather, Biol. Reprod. 23:243-251(1980)); monkey kidney cells (CV1 ATCC CCL 70); African green monkeykidney cells (VERO-76, ATCC CRL-1587); human cervical carcinoma cells(HELA, ATCC CCL 2); canine kidney cells (MDCK, ATCC CCL 34); buffalo ratliver cells (BRL 3A, ATCC CRL 1442); human lung cells (W138, ATCC CCL75); human liver cells (Hep G2, HB 8065); mouse mammary tumor (MMT060562, ATCC CCL51); TRI cells (Mather et al., Annals N.Y. Acad. Sci.383:44-68 (1982)); MRC 5 cells; FS4 cells; and a human hepatoma line(Hep G2).

Host cells are transformed with the above-described expression orcloning vectors for anti-TAT antibody or TAT polypeptide production andcultured in conventional nutrient media modified as appropriate forinducing promoters, selecting transformants, or amplifying the genesencoding the desired sequences.

3. Selection and Use of a Replicable Vector

The nucleic acid (e.g., cDNA or genomic DNA) encoding anti-TAT antibodyor TAT polypeptide may be inserted into a replicable vector for cloning(amplification of the DNA) or for expression. Various vectors arepublicly available. The vector may, for example, be in the form of aplasmid, cosmid, viral particle, or phage. The appropriate nucleic acidsequence may be inserted into the vector by a variety of procedures. Ingeneral, DNA is inserted into an appropriate restriction endonucleasesite(s) using techniques known in the art. Vector components generallyinclude, but are not limited to, one or more of a signal sequence, anorigin of replication, one or more marker genes, an enhancer element, apromoter, and a transcription termination sequence. Construction ofsuitable vectors containing one or more of these components employsstandard ligation techniques which are known to the skilled artisan.

The TAT may be produced recombinantly not only directly, but also as afusion polypeptide with a heterologous polypeptide, which may be asignal sequence or other polypeptide having a specific cleavage site atthe N-terminus of the mature protein or polypeptide. In general, thesignal sequence may be a component of the vector, or it may be a part ofthe anti-TAT antibody- or TAT polypeptide-encoding DNA that is insertedinto the vector. The signal sequence may be a prokaryotic signalsequence selected, for example, from the group of the alkalinephosphatase, penicillinase, lpp, or heat-stable enterotoxin II leaders.For yeast secretion the signal sequence may be, e.g., the yeastinvertase leader, alpha factor leader (including Saccharomyces andKluyveromyces α-factor leaders, the latter described in U.S. Pat. No.5,010,182), or acid phosphatase leader, the C. albicans glucoamylaseleader (EP 362,179 published 4 Apr. 1990), or the signal described in WO90/13646 published 15 Nov. 1990. In mammalian cell expression, mammaliansignal sequences may be used to direct secretion of the protein, such assignal sequences from secreted polypeptides of the same or relatedspecies, as well as viral secretory leaders.

Both expression and cloning vectors contain a nucleic acid sequence thatenables the vector to replicate in one or more selected host cells. Suchsequences are well known for a variety of bacteria, yeast, and viruses.The origin of replication from the plasmid pBR322 is suitable for mostGram-negative bacteria, the 2μ plasmid origin is suitable for yeast, andvarious viral origins (SV40, polyoma, adenovirus, VSV or BPV) are usefulfor cloning vectors in mammalian cells.

Expression and cloning vectors will typically contain a selection gene,also termed a selectable marker. Typical selection genes encode proteinsthat (a) confer resistance to antibiotics or other toxins, e.g.,ampicillin, neomycin, methotrexate, or tetracycline, (b) complementauxotrophic deficiencies, or (c) supply critical nutrients not availablefrom complex media, e.g., the gene encoding D-alanine racemase forBacilli.

An example of suitable selectable markers for mammalian cells are thosethat enable the identification of cells competent to take up theanti-TAT antibody- or TAT polypeptide-encoding nucleic acid, such asDHFR or thymidine kinase. An appropriate host cell when wild-type DHFRis employed is the CHO cell line deficient in DHFR activity, preparedand propagated as described by Urlaub et al., Proc. Natl. Acad. Sci.USA, 77:4216 (1980). A suitable selection gene for use in yeast is thetrp1 gene present in the yeast plasmid YRp7 [Stinchcomb et al., Nature,282:39 (1979); Kingsman et al., Gene, 7:141 (1979); Tschemper et al.,Gene, 10:157 (1980)]. The trp1 gene provides a selection marker for amutant strain of yeast lacking the ability to grow in tryptophan, forexample, ATCC No. 44076 or PEP4-1 [Jones, Genetics, 85:12 (1977)].

Expression and cloning vectors usually contain a promoter operablylinked to the anti-TAT antibody- or TAT polypeptide-encoding nucleicacid sequence to direct mRNA synthesis. Promoters recognized by avariety of potential host cells are well known. Promoters suitable foruse with prokaryotic hosts include the β-lactamase and lactose promotersystems [Chang et al., Nature, 275:615 (1978); Goeddel et al., Nature,281:544 (1979)], alkaline phosphatase, a tryptophan (trp) promotersystem [Goeddel, Nucleic Acids Res., 8:4057 (1980); EP 36,776], andhybrid promoters such as the tac promoter [deBoer et al., Proc. Natl.Acad. Sci. USA, 80:21-25 (1983)]. Promoters for use in bacterial systemsalso will contain a Shine-Dalgarno (S.D.) sequence operably linked tothe DNA encoding anti-TAT antibody or TAT polypeptide.

Examples of suitable promoting sequences for use with yeast hostsinclude the promoters for 3-phosphoglycerate kinase [Hitzeman et al., J.Biol. Chem., 255:2073 (1980)] or other glycolytic enzymes [Hess et al.,J. Adv. Enzyme Reg., 7:149 (1968); Holland, Biochemistry, 17:4900(1978)], such as enolase, glyceraldehyde-3-phosphate dehydrogenase,hexokinase, pyruvate decarboxylase, phosphofructokinase,glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvatekinase, triosephosphate isomerase, phosphoglucose isomerase, andglucokinase.

Other yeast promoters, which are inducible promoters having theadditional advantage of transcription controlled by growth conditions,are the promoter regions for alcohol dehydrogenase 2, isocytochrome C,acid phosphatase, degradative enzymes associated with nitrogenmetabolism, metallothionein, glyceraldehyde-3-phosphate dehydrogenase,and enzymes responsible for maltose and galactose utilization. Suitablevectors and promoters for use in yeast expression are further describedin EP 73,657.

Anti-TAT antibody or TAT polypeptide transcription from vectors inmammalian host cells is controlled, for example, by promoters obtainedfrom the genomes of viruses such as polyoma virus, fowlpox virus (UK2,211,504 published 5 Jul. 1989), adenovirus (such as Adenovirus 2),bovine papilloma virus, avian sarcoma virus, cytomegalovirus, aretrovirus, hepatitis-B virus and Simian Virus 40 (SV40), fromheterologous mammalian promoters, e.g., the actin promoter or animmunoglobulin promoter, and from heat-shock promoters, provided suchpromoters are compatible with the host cell systems.

Transcription of a DNA encoding the anti-TAT antibody or TAT polypeptideby higher eukaryotes may be increased by inserting an enhancer sequenceinto the vector. Enhancers are cis-acting elements of DNA, usually aboutfrom 10 to 300 bp, that act on a promoter to increase its transcription.Many enhancer sequences are now known from mammalian genes (globin,elastase, albumin, α-fetoprotein, and insulin). Typically, however, onewill use an enhancer from a eukaryotic cell virus. Examples include theSV40 enhancer on the late side of the replication origin (bp 100-270),the cytomegalovirus early promoter enhancer, the polyoma enhancer on thelate side of the replication origin, and adenovirus enhancers. Theenhancer may be spliced into the vector at a position 5′ or 3′ to theanti-TAT antibody or TAT polypeptide coding sequence, but is preferablylocated at a site 5′ from the promoter.

Expression vectors used in eukaryotic host cells (yeast, fungi, insect,plant, animal, human, or nucleated cells from other multicellularorganisms) will also contain sequences necessary for the termination oftranscription and for stabilizing the mRNA. Such sequences are commonlyavailable from the 5′ and, occasionally 3′, untranslated regions ofeukaryotic or viral DNAs or cDNAs. These regions contain nucleotidesegments transcribed as polyadenylated fragments in the untranslatedportion of the mRNA encoding anti-TAT antibody or TAT polypeptide.

Still other methods, vectors, and host cells suitable for adaptation tothe synthesis of anti-TAT antibody or TAT polypeptide in recombinantvertebrate cell culture are described in Gething et al., Nature,293:620-625 (1981); Mantei et al., Nature, 281:40-46 (1979); EP 117,060;and EP 117,058.

4. Culturing the Host Cells

The host cells used to produce the anti-TAT antibody or TAT polypeptideof this invention may be cultured in a variety of media. Commerciallyavailable media such as Ham's F 10 (Sigma), Minimal Essential Medium((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle'sMedium ((DMEM), Sigma) are suitable for culturing the host cells. Inaddition, any of the media described in Ham et al., Meth. Enz. 58:44(1979), Barnes et al., Anal. Biochem. 102:255 (1980), U.S. Pat. No.4,767,704; 4,657,866; 4,927,762; 4,560,655; or 5,122,469; WO 90/03430;WO 87/00195; or U.S. Pat. Re. 30,985 may be used as culture media forthe host cells. Any of these media may be supplemented as necessary withhormones and/or other growth factors (such as insulin, transferrin, orepidermal growth factor), salts (such as sodium chloride, calcium,magnesium, and phosphate), buffers (such as HEPES), nucleotides (such asadenosine and thymidine), antibiotics (such as GENTAMYCIN™ drug), traceelements (defined as inorganic compounds usually present at finalconcentrations in the micromolar range), and glucose or an equivalentenergy source. Any other necessary supplements may also be included atappropriate concentrations that would be known to those skilled in theart. The culture conditions, such as temperature, pH, and the like, arethose previously used with the host cell selected for expression, andwill be apparent to the ordinarily skilled artisan.

5. Detecting Gene Amplification/Expression

Gene amplification and/or expression may be measured in a sampledirectly, for example, by conventional Southern blotting, Northernblotting to quantitate the transcription of mRNA [Thomas, Proc. Natl.Acad. Sci. USA, 77:5201-5205 (1980)], dot blotting (DNA analysis), or insitu hybridization, using an appropriately labeled probe, based on thesequences provided herein. Alternatively, antibodies may be employedthat can recognize specific duplexes, including DNA duplexes, RNAduplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Theantibodies in turn may be labeled and the assay may be carried out wherethe duplex is bound to a surface, so that upon the formation of duplexon the surface, the presence of antibody bound to the duplex can bedetected.

Gene expression, alternatively, may be measured by immunologicalmethods, such as immunohistochemical staining of cells or tissuesections and assay of cell culture or body fluids, to quantitatedirectly the expression of gene product. Antibodies useful forimmunohistochemical staining and/or assay of sample fluids may be eithermonoclonal or polyclonal, and may be prepared in any mammal.Conveniently, the antibodies may be prepared against a native sequenceTAT polypeptide or against a synthetic peptide based on the DNAsequences provided herein or against exogenous sequence fused to TAT DNAand encoding a specific antibody epitope.

6. Purification of Anti-TAT Antibody and TAT Polypeptide

Forms of anti-TAT antibody and TAT polypeptide may be recovered fromculture medium or from host cell lysates. If membrane-bound, it can bereleased from the membrane using a suitable detergent solution (e.g.Triton-X 100) or by enzymatic cleavage. Cells employed in expression ofanti-TAT antibody and TAT polypeptide can be disrupted by variousphysical or chemical means, such as freeze-thaw cycling, sonication,mechanical disruption, or cell lysing agents.

It may be desired to purify anti-TAT antibody and TAT polypeptide fromrecombinant cell proteins or polypeptides. The following procedures areexemplary of suitable purification procedures: by fractionation on anion-exchange column; ethanol precipitation; reverse phase HPLC;chromatography on silica or on a cation-exchange resin such as DEAE;chromatofocusing; SDS-PAGE; ammonium sulfate precipitation; gelfiltration using, for example, Sephadex G-75; protein A Sepharosecolumns to remove contaminants such as IgG; and metal chelating columnsto bind epitope-tagged forms of the anti-TAT antibody and TATpolypeptide. Various methods of protein purification may be employed andsuch methods are known in the art and described for example inDeutscher, Methods in Enzymology, 182 (1990); Scopes, ProteinPurification: Principles and Practice, Springer-Verlag, New York (1982).The purification step(s) selected will depend, for example, on thenature of the production process used and the particular anti-TATantibody or TAT polypeptide produced.

When using recombinant techniques, the antibody can be producedintracellularly, in the periplasmic space, or directly secreted into themedium. If the antibody is produced intracellularly, as a first step,the particulate debris, either host cells or lysed fragments, areremoved, for example, by centrifugation or ultrafiltration. Carter etal., Bio/Technology 10:163-167 (1992) describe a procedure for isolatingantibodies which are secreted to the periplasmic space of E. coli.Briefly, cell paste is thawed in the presence of sodium acetate (pH3.5), EDTA, and phenylmethylsulfonylfluoride (PMSF) over about 30 min.Cell debris can be removed by centrifugation. Where the antibody issecreted into the medium, supernatants from such expression systems aregenerally first concentrated using a commercially available proteinconcentration filter, for example, an Amicon or Millipore Pelliconultrafiltration unit. A protease inhibitor such as PMSF may be includedin any of the foregoing steps to inhibit proteolysis and antibiotics maybe included to prevent the growth of adventitious contaminants.

The antibody composition prepared from the cells can be purified using,for example, hydroxylapatite chromatography, gel electrophoresis,dialysis, and affinity chromatography, with affinity chromatographybeing the preferred purification technique. The suitability of protein Aas an affinity ligand depends on the species and isotype of anyimmunoglobulin Fc domain that is present in the antibody. Protein A canbe used to purify antibodies that are based on human γ1, γ2 or γ4 heavychains (Lindmark et al., J. Immunol. Meth. 62:1-13 (1983)). Protein G isrecommended for all mouse isotypes and for human γ3 (Guss et al., EMBOJ. 5:15671575 (1986)). The matrix to which the affinity ligand isattached is most often agarose, but other matrices are available.Mechanically stable matrices such as controlled pore glass orpoly(styrenedivinyl)benzene allow for faster flow rates and shorterprocessing times than can be achieved with agarose. Where the antibodycomprises a C_(H)3 domain, the Bakerbond ABX™ resin (J. T. Baker,Phillipsburg, N.J.) is useful for purification. Other techniques forprotein purification such as fractionation on an ion-exchange column,ethanol precipitation, Reverse Phase HPLC, chromatography on silica,chromatography on heparin SEPHAROSE™ chromatography on an anion orcation exchange resin (such as a polyaspartic acid column),chromatofocusing, SDS-PAGE, and ammonium sulfate precipitation are alsoavailable depending on the antibody to be recovered.

Following any preliminary purification step(s), the mixture comprisingthe antibody of interest and contaminants may be subjected to low pHhydrophobic interaction chromatography using an elution buffer at a pHbetween about 2.5-4.5, preferably performed at low salt concentrations(e.g., from about 0-0.25M salt).

J. Pharmaceutical Formulations

Therapeutic formulations of the anti-TAT antibodies, TAT bindingoligopeptides, TAT binding organic molecules and/or TAT polypeptidesused in accordance with the present invention are prepared for storageby mixing the antibody, polypeptide, oligopeptide or organic moleculehaving the desired degree of purity with optional pharmaceuticallyacceptable carriers, excipients or stabilizers (Remington'sPharmaceutical Sciences 16th edition, Osol, A. Ed. (1980)), in the formof lyophilized formulations or aqueous solutions. Acceptable carriers,excipients, or stabilizers are nontoxic to recipients at the dosages andconcentrations employed, and include buffers such as acetate, Tris,phosphate, citrate, and other organic acids; antioxidants includingascorbic acid and methionine; preservatives (such asoctadecyldimethylbenzyl ammonium chloride; hexamethonium chloride;benzalkonium chloride, benzethonium chloride; phenol, butyl or benzylalcohol; alkyl parabens such as methyl or propyl paraben; catechol;resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecularweight (less than about 10 residues) polypeptides; proteins, such asserum albumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids such as glycine, glutamine,asparagine, histidine, arginine, or lysine; monosaccharides,disaccharides, and other carbohydrates including glucose, mannose, ordextrins; chelating agents such as EDTA; tonicifiers such as trehaloseand sodium chloride; sugars such as sucrose, mannitol, trehalose orsorbitol; surfactant such as polysorbate; salt-forming counter-ions suchas sodium; metal complexes (e.g., Zn-protein complexes); and/ornon-ionic surfactants such as TWEEN®, PLURONICS® or polyethylene glycol(PEG). The antibody preferably comprises the antibody at a concentrationof between 5-200 mg/ml, preferably between 10-100 mg/ml.

The formulations herein may also contain more than one active compoundas necessary for the particular indication being treated, preferablythose with complementary activities that do not adversely affect eachother. For example, in addition to an anti-TAT antibody, TAT bindingoligopeptide, or TAT binding organic molecule, it may be desirable toinclude in the one formulation, an additional antibody, e.g., a secondanti-TAT antibody which binds a different epitope on the TATpolypeptide, or an antibody to some other target such as a growth factorthat affects the growth of the particular cancer. Alternatively, oradditionally, the composition may further comprise a chemotherapeuticagent, cytotoxic agent, cytokine, growth inhibitory agent, anti-hormonalagent, and/or cardioprotectant. Such molecules are suitably present incombination in amounts that are effective for the purpose intended.

The active ingredients may also be entrapped in microcapsules prepared,for example, by coacervation techniques or by interfacialpolymerization, for example, hydroxymethylcellulose orgelatin-microcapsules and poly-(methylmethacylate) microcapsules,respectively, in colloidal drug delivery systems (for example,liposomes, albumin microspheres, microemulsions, nano-particles andnanocapsules) or in macroemulsions. Such techniques are disclosed inRemington's Pharmaceutical Sciences, 16th edition, Osol, A. Ed. (1980).

Sustained-release preparations may be prepared. Suitable examples ofsustained-release preparations include semi-permeable matrices of solidhydrophobic polymers containing the antibody, which matrices are in theform of shaped articles, e.g., films, or microcapsules. Examples ofsustained-release matrices include polyesters, hydrogels (for example,poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides(U.S. Pat. No. 3,773,919), copolymers of L-glutamic acid and γethyl-L-glutamate, non-degradable ethylene-vinyl acetate, degradablelactic acid-glycolic acid copolymers such as the LUPRON DEPOT®(injectable microspheres composed of lactic acid-glycolic acid copolymerand leuprolide acetate), and poly-D-(−)-3-hydroxybutyric acid.

The formulations to be used for in vivo administration must be sterile.This is readily accomplished by filtration through sterile filtrationmembranes.

K. Diagnosis and Treatment with Anti-TAT Antibodies, TAT BindingOligopeptides and TAT Binding Organic Molecules

To determine TAT expression in the cancer, various diagnostic assays areavailable. In one embodiment, TAT polypeptide overexpression may beanalyzed by immunohistochemistry (IHC). Parrafin embedded tissuesections from a tumor biopsy may be subjected to the IHC assay andaccorded a TAT protein staining intensity criteria as follows:

Score 0— no staining is observed or membrane staining is observed inless than 10% of tumor cells.

Score 1+—a faint/barely perceptible membrane staining is detected inmore than 10% of the tumor cells. The cells are only stained in part oftheir membrane.

Score 2+—a weak to moderate complete membrane staining is observed inmore than 10% of the tumor cells.

Score 3+—a moderate to strong complete membrane staining is observed inmore than 10% of the tumor cells.

Those tumors with 0 or 1+scores for TAT polypeptide expression may becharacterized as not overexpressing TAT, whereas those tumors with 2+ or3+ scores may be characterized as overexpressing TAT.

Alternatively, or additionally, FISH assays such as the INFORM® (sold byVentana, Arizona) or PATHVISION® (Vysis, Illinois) may be carried out onformalin-fixed, paraffin-embedded tumor tissue to determine the extent(if any) of TAT overexpression in the tumor.

TAT overexpression or amplification may be evaluated using an in vivodiagnostic assay, e.g., by administering a molecule (such as anantibody, oligopeptide or organic molecule) which binds the molecule tobe detected and is tagged with a detectable label (e.g., a radioactiveisotope or a fluorescent label) and externally scanning the patient forlocalization of the label.

As described above, the anti-TAT antibodies, oligopeptides and organicmolecules of the invention have various non-therapeutic applications.The anti-TAT antibodies, oligopeptides and organic molecules of thepresent invention can be useful for diagnosis and staging of TATpolypeptide-expressing cancers (e.g., in radioimaging). The antibodies,oligopeptides and organic molecules are also useful for purification orimmunoprecipitation of TAT polypeptide from cells, for detection andquantitation of TAT polypeptide in vitro, e.g., in an ELISA or a Westernblot, to kill and eliminate TAT-expressing cells from a population ofmixed cells as a step in the purification of other cells.

Currently, depending on the stage of the cancer, cancer treatmentinvolves one or a combination of the following therapies: surgery toremove the cancerous tissue, radiation therapy, and chemotherapy.Anti-TAT antibody, oligopeptide or organic molecule therapy may beespecially desirable in elderly patients who do not tolerate thetoxicity and side effects of chemotherapy well and in metastatic diseasewhere radiation therapy has limited usefulness. The tumor targetinganti-TAT antibodies, oligopeptides and organic molecules of theinvention are useful to alleviate TAT-expressing cancers upon initialdiagnosis of the disease or during relapse. For therapeuticapplications, the anti-TAT antibody, oligopeptide or organic moleculecan be used alone, or in combination therapy with, e.g., hormones,antiangiogens, or radiolabelled compounds, or with surgery, cryotherapy,and/or radiotherapy. Anti-TAT antibody, oligopeptide or organic moleculetreatment can be administered in conjunction with other forms ofconventional therapy, either consecutively with, pre- orpost-conventional therapy. Chemotherapeutic drugs such as TAXOTERE®(docetaxel), TAXOL® (palictaxel), estramustine and mitoxantrone are usedin treating cancer, in particular, in good risk patients. In the presentmethod of the invention for treating or alleviating cancer, the cancerpatient can be administered anti-TAT antibody, oligopeptide or organicmolecule in conjunction with treatment with the one or more of thepreceding chemotherapeutic agents. In particular, combination therapywith palictaxel and modified derivatives (see, e.g., EP0600517) iscontemplated. The anti-TAT antibody, oligopeptide or organic moleculewill be administered with a therapeutically effective dose of thechemotherapeutic agent. In another embodiment, the anti-TAT antibody,oligopeptide or organic molecule is administered in conjunction withchemotherapy to enhance the activity and efficacy of thechemotherapeutic agent, e.g., paclitaxel. The Physicians' Desk Reference(PDR) discloses dosages of these agents that have been used in treatmentof various cancers. The dosing regimen and dosages of theseaforementioned chemotherapeutic drugs that are therapeutically effectivewill depend on the particular cancer being treated, the extent of thedisease and other factors familiar to the physician of skill in the artand can be determined by the physician.

In one particular embodiment, a conjugate comprising an anti-TATantibody, oligopeptide or organic molecule conjugated with a cytotoxicagent is administered to the patient. Preferably, the immunoconjugatebound to the TAT protein is internalized by the cell, resulting inincreased therapeutic efficacy of the immunoconjugate in killing thecancer cell to which it binds. In a preferred embodiment, the cytotoxicagent targets or interferes with the nucleic acid in the cancer cell.Examples of such cytotoxic agents are described above and includemaytansinoids, calicheamicins, ribonucleases and DNA endonucleases.

The anti-TAT antibodies, oligopeptides, organic molecules or toxinconjugates thereof are administered to a human patient, in accord withknown methods, such as intravenous administration, e.g., as a bolus orby continuous infusion over a period of time, by intramuscular,intraperitoneal, intracerobrospinal, subcutaneous, intra-articular,intrasynovial, intrathecal, oral, topical, or inhalation routes.Intravenous or subcutaneous administration of the antibody, oligopeptideor organic molecule is preferred.

Other therapeutic regimens may be combined with the administration ofthe anti-TAT antibody, oligopeptide or organic molecule. The combinedadministration includes co-administration, using separate formulationsor a single pharmaceutical formulation, and consecutive administrationin either order, wherein preferably there is a time period while both(or all) active agents simultaneously exert their biological activities.Preferably such combined therapy results in a synergistic therapeuticeffect.

It may also be desirable to combine administration of the anti-TATantibody or antibodies, oligopeptides or organic molecules, withadministration of an antibody directed against another tumor antigenassociated with the particular cancer.

In another embodiment, the therapeutic treatment methods of the presentinvention involves the combined administration of an anti-TAT antibody(or antibodies), oligopeptides or organic molecules and one or morechemotherapeutic agents or growth inhibitory agents, includingco-administration of cocktails of different chemotherapeutic agents.Chemotherapeutic agents include estramustine phosphate, prednimustine,cisplatin, 5-fluorouracil, melphalan, cyclophosphamide, hydroxyurea andhydroxyureataxanes (such as paclitaxel and doxetaxel) and/oranthracycline antibiotics. Preparation and dosing schedules for suchchemotherapeutic agents may be used according to manufacturers'instructions or as determined empirically by the skilled practitioner.Preparation and dosing schedules for such chemotherapy are alsodescribed in Chemotherapy Service Ed., M. C. Perry, Williams & Wilkins,Baltimore, Md. (1992).

The antibody, oligopeptide or organic molecule may be combined with ananti-hormonal compound; e.g., an anti-estrogen compound such astamoxifen; an anti-progesterone such as onapristone (see, EP 616 812);or an anti-androgen such as flutamide, in dosages known for suchmolecules. Where the cancer to be treated is androgen independentcancer, the patient may previously have been subjected to anti-androgentherapy and, after the cancer becomes androgen independent, the anti-TATantibody, oligopeptide or organic molecule (and optionally other agentsas described herein) may be administered to the patient.

Sometimes, it may be beneficial to also co-administer a cardioprotectant(to prevent or reduce myocardial dysfunction associated with thetherapy) or one or more cytokines to the patient. In addition to theabove therapeutic regimes, the patient may be subjected to surgicalremoval of cancer cells and/or radiation therapy, before, simultaneouslywith, or post antibody, oligopeptide or organic molecule therapy.Suitable dosages for any of the above co-administered agents are thosepresently used and may be lowered due to the combined action (synergy)of the agent and anti-TAT antibody, oligopeptide or organic molecule.

For the prevention or treatment of disease, the dosage and mode ofadministration will be chosen by the physician according to knowncriteria. The appropriate dosage of antibody, oligopeptide or organicmolecule will depend on the type of disease to be treated, as definedabove, the severity and course of the disease, whether the antibody,oligopeptide or organic molecule is administered for preventive ortherapeutic purposes, previous therapy, the patient's clinical historyand response to the antibody, oligopeptide or organic molecule, and thediscretion of the attending physician. The antibody, oligopeptide ororganic molecule is suitably administered to the patient at one time orover a series of treatments. Preferably, the antibody, oligopeptide ororganic molecule is administered by intravenous infusion or bysubcutaneous injections. Depending on the type and severity of thedisease, about 1 μg/kg to about 50 mg/kg body weight (e.g., about 0.1-15mg/kg/dose) of antibody can be an initial candidate dosage foradministration to the patient, whether, for example, by one or moreseparate administrations, or by continuous infusion. A dosing regimencan comprise administering an initial loading dose of about 4 mg/kg,followed by a weekly maintenance dose of about 2 mg/kg of the anti-TATantibody. However, other dosage regimens may be useful. A typical dailydosage might range from about 1 μg/kg to 100 mg/kg or more, depending onthe factors mentioned above. For repeated administrations over severaldays or longer, depending on the condition, the treatment is sustaineduntil a desired suppression of disease symptoms occurs. The progress ofthis therapy can be readily monitored by conventional methods and assaysand based on criteria known to the physician or other persons of skillin the art.

Aside from administration of the antibody protein to the patient, thepresent application contemplates administration of the antibody by genetherapy. Such administration of nucleic acid encoding the antibody isencompassed by the expression “administering a therapeutically effectiveamount of an antibody”. See, for example, WO96/07321 published Mar. 14,1996 concerning the use of gene therapy to generate intracellularantibodies.

There are two major approaches to getting the nucleic acid (optionallycontained in a vector) into the patient's cells; in vivo and ex vivo.For in vivo delivery the nucleic acid is injected directly into thepatient, usually at the site where the antibody is required. For ex vivotreatment, the patient's cells are removed, the nucleic acid isintroduced into these isolated cells and the modified cells areadministered to the patient either directly or, for example,encapsulated within porous membranes which are implanted into thepatient (see, e.g., U.S. Pat. Nos. 4,892,538 and 5,283,187). There are avariety of techniques available for introducing nucleic acids intoviable cells. The techniques vary depending upon whether the nucleicacid is transferred into cultured cells in vitro, or in vivo in thecells of the intended host. Techniques suitable for the transfer ofnucleic acid into mammalian cells in vitro include the use of liposomes,electroporation, microinjection, cell fusion, DEAE-dextran, the calciumphosphate precipitation method, etc. A commonly used vector for ex vivodelivery of the gene is a retroviral vector.

The currently preferred in vivo nucleic acid transfer techniques includetransfection with viral vectors (such as adenovirus, Herpes simplex Ivirus, or adeno-associated virus) and lipid-based systems (useful lipidsfor lipid-mediated transfer of the gene are DOTMA, DOPE and DC-Chol, forexample). For review of the currently known gene marking and genetherapy protocols see Anderson et al., Science 256:808-813 (1992). Seealso WO 93/25673 and the references cited therein.

The anti-TAT antibodies of the invention can be in the different formsencompassed by the definition of “antibody” herein. Thus, the antibodiesinclude full length or intact antibody, antibody fragments, nativesequence antibody or amino acid variants, humanized, chimeric or fusionantibodies, immunoconjugates, and functional fragments thereof. Infusion antibodies an antibody sequence is fused to a heterologouspolypeptide sequence. The antibodies can be modified in the Fc region toprovide desired effector functions. As discussed in more detail in thesections herein, with the appropriate Fc regions, the naked antibodybound on the cell surface can induce cytotoxicity, e.g., viaantibody-dependent cellular cytotoxicity (ADCC) or by recruitingcomplement in complement dependent cytotoxicity, or some othermechanism. Alternatively, where it is desirable to eliminate or reduceeffector function, so as to minimize side effects or therapeuticcomplications, certain other Fc regions may be used.

In one embodiment, the antibody competes for binding or bindsubstantially to, the same epitope as the antibodies of the invention.Antibodies having the biological characteristics of the present anti-TATantibodies of the invention are also contemplated, specificallyincluding the in vivo tumor targeting and any cell proliferationinhibition or cytotoxic characteristics.

Methods of producing the above antibodies are described in detailherein.

The present anti-TAT antibodies, oligopeptides and organic molecules areuseful for treating a TAT-expressing cancer or alleviating one or moresymptoms of the cancer in a mammal. Such a cancer includes prostatecancer, cancer of the urinary tract, lung cancer, breast cancer, coloncancer and ovarian cancer, more specifically, prostate adenocarcinoma,renal cell carcinomas, colorectal adenocarcinomas, lung adenocarcinomas,lung squamous cell carcinomas, and pleural mesothelioma. The cancersencompass metastatic cancers of any of the preceding. The antibody,oligopeptide or organic molecule is able to bind to at least a portionof the cancer cells that express TAT polypeptide in the mammal. In apreferred embodiment, the antibody, oligopeptide or organic molecule iseffective to destroy or kill TAT-expressing tumor cells or inhibit thegrowth of such tumor cells, in vitro or in vivo, upon binding to TATpolypeptide on the cell. Such an antibody includes a naked anti-TATantibody (not conjugated to any agent). Naked antibodies that havecytotoxic or cell growth inhibition properties can be further harnessedwith a cytotoxic agent to render them even more potent in tumor celldestruction. Cytotoxic properties can be conferred to an anti-TATantibody by, e.g., conjugating the antibody with a cytotoxic agent, toform an immunoconjugate as described herein. The cytotoxic agent or agrowth inhibitory agent is preferably a small molecule. Toxins such ascalicheamicin or a maytansinoid and analogs or derivatives thereof, arepreferable.

The invention provides a composition comprising an anti-TAT antibody,oligopeptide or organic molecule of the invention, and a carrier. Forthe purposes of treating cancer, compositions can be administered to thepatient in need of such treatment, wherein the composition can compriseone or more anti-TAT antibodies present as an immunoconjugate or as thenaked antibody. In a further embodiment, the compositions can comprisethese antibodies, oligopeptides or organic molecules in combination withother therapeutic agents such as cytotoxic or growth inhibitory agents,including chemotherapeutic agents. The invention also providesformulations comprising an anti-TAT antibody, oligopeptide or organicmolecule of the invention, and a carrier. In one embodiment, theformulation is a therapeutic formulation comprising a pharmaceuticallyacceptable carrier.

Another aspect of the invention is isolated nucleic acids encoding theanti-TAT antibodies. Nucleic acids encoding both the H and L chains andespecially the hypervariable region residues, chains which encode thenative sequence antibody as well as variants, modifications andhumanized versions of the antibody, are encompassed.

The invention also provides methods useful for treating a TATpolypeptide-expressing cancer or alleviating one or more symptoms of thecancer in a mammal, comprising administering a therapeutically effectiveamount of an anti-TAT antibody, oligopeptide or organic molecule to themammal. The antibody, oligopeptide or organic molecule therapeuticcompositions can be administered short term (acute) or chronic, orintermittent as directed by physician. Also provided are methods ofinhibiting the growth of, and killing a TAT polypeptide-expressing cell.

The invention also provides kits and articles of manufacture comprisingat least one anti-TAT antibody, oligopeptide or organic molecule. Kitscontaining anti-TAT antibodies, oligopeptides or organic molecules finduse, e.g., for TAT cell killing assays, for purification orimmunoprecipitation of TAT polypeptide from cells. For example, forisolation and purification of TAT, the kit can contain an anti-TATantibody, oligopeptide or organic molecule coupled to beads (e.g.,sepharose beads). Kits can be provided which contain the antibodies,oligopeptides or organic molecules for detection and quantitation of TATin vitro, e.g., in an ELISA or a Western blot. Such antibody,oligopeptide or organic molecule useful for detection may be providedwith a label such as a fluorescent or radiolabel.

L. Articles of Manufacture and Kits

Another embodiment of the invention is an article of manufacturecontaining materials useful for the treatment of anti-TAT expressingcancer. The article of manufacture comprises a container and a label orpackage insert on or associated with the container. Suitable containersinclude, for example, bottles, vials, syringes, etc. The containers maybe formed from a variety of materials such as glass or plastic. Thecontainer holds a composition which is effective for treating the cancercondition and may have a sterile access port (for example the containermay be an intravenous solution bag or a vial having a stopper pierceableby a hypodermic injection needle). At least one active agent in thecomposition is an anti-TAT antibody, oligopeptide or organic molecule ofthe invention. The label or package insert indicates that thecomposition is used for treating cancer. The label or package insertwill further comprise instructions for administering the antibody,oligopeptide or organic molecule composition to the cancer patient.Additionally, the article of manufacture may further comprise a secondcontainer comprising a pharmaceutically-acceptable buffer, such asbacteriostatic water for injection (BWFI), phosphate-buffered saline,Ringer's solution and dextrose solution. It may further include othermaterials desirable from a commercial and user standpoint, includingother buffers, diluents, filters, needles, and syringes.

Kits are also provided that are useful for various purposes, e.g., forTAT-expressing cell killing assays, for purification orimmunoprecipitation of TAT polypeptide from cells. For isolation andpurification of TAT polypeptide, the kit can contain an anti-TATantibody, oligopeptide or organic molecule coupled to beads (e.g.,sepharose beads). Kits can be provided which contain the antibodies,oligopeptides or organic molecules for detection and quantitation of TATpolypeptide in vitro, e.g., in an ELISA or a Western blot. As with thearticle of manufacture, the kit comprises a container and a label orpackage insert on or associated with the container. The container holdsa composition comprising at least one anti-TAT antibody, oligopeptide ororganic molecule of the invention. Additional containers may be includedthat contain, e.g., diluents and buffers, control antibodies. The labelor package insert may provide a description of the composition as wellas instructions for the intended in vitro or diagnostic use.

M. Uses for TAT Polypeptides and TAT-Polypeptide Encoding Nucleic Acids

Nucleotide sequences (or their complement) encoding TAT polypeptideshave various applications in the art of molecular biology, includinguses as hybridization probes, in chromosome and gene mapping and in thegeneration of anti-sense RNA and DNA probes. TAT-encoding nucleic acidwill also be useful for the preparation of TAT polypeptides by therecombinant techniques described herein, wherein those TAT polypeptidesmay find use, for example, in the preparation of anti-TAT antibodies asdescribed herein.

The full-length native sequence TAT gene, or portions thereof, may beused as hybridization probes for a cDNA library to isolate thefull-length TAT cDNA or to isolate still other cDNAs (for instance,those encoding naturally-occurring variants of TAT or TAT from otherspecies) which have a desired sequence identity to the native TATsequence disclosed herein. Optionally, the length of the probes will beabout 20 to about 50 bases. The hybridization probes may be derived fromat least partially novel regions of the full length native nucleotidesequence wherein those regions may be determined without undueexperimentation or from genomic sequences including promoters, enhancerelements and introns of native sequence TAT. By way of example, ascreening method will comprise isolating the coding region of the TATgene using the known DNA sequence to synthesize a selected probe ofabout 40 bases. Hybridization probes may be labeled by a variety oflabels, including radionucleotides such as ³²P or ³⁵S, or enzymaticlabels such as alkaline phosphatase coupled to the probe viaavidin/biotin coupling systems. Labeled probes having a sequencecomplementary to that of the TAT gene of the present invention can beused to screen libraries of human cDNA, genomic DNA or mRNA to determinewhich members of such libraries the probe hybridizes to. Hybridizationtechniques are described in further detail in the Examples below. AnyEST sequences disclosed in the present application may similarly beemployed as probes, using the methods disclosed herein.

Other useful fragments of the TAT-encoding nucleic acids includeantisense or sense oligonucleotides comprising a singe-stranded nucleicacid sequence (either RNA or DNA) capable of binding to target TAT mRNA(sense) or TAT DNA (antisense) sequences. Antisense or senseoligonucleotides, according to the present invention, comprise afragment of the coding region of TAT DNA. Such a fragment generallycomprises at least about 14 nucleotides, preferably from about 14 to 30nucleotides. The ability to derive an antisense or a senseoligonucleotide, based upon a cDNA sequence encoding a given protein isdescribed in, for example, Stein and Cohen (Cancer Res. 48:2659, 1988)and van der Krol et al. (BioTechniques 6:958, 1988).

Binding of antisense or sense oligonucleotides to target nucleic acidsequences results in the formation of duplexes that block transcriptionor translation of the target sequence by one of several means, includingenhanced degradation of the duplexes, premature termination oftranscription or translation, or by other means. Such methods areencompassed by the present invention. The antisense oligonucleotidesthus may be used to block expression of TAT proteins, wherein those TATproteins may play a role in the induction of cancer in mammals.Antisense or sense oligonucleotides further comprise oligonucleotideshaving modified sugar-phosphodiester backbones (or other sugar linkages,such as those described in WO 91/06629) and wherein such sugar linkagesare resistant to endogenous nucleases. Such oligonucleotides withresistant sugar linkages are stable in vivo (i.e., capable of resistingenzymatic degradation) but retain sequence specificity to be able tobind to target nucleotide sequences.

Other examples of sense or antisense oligonucleotides include thoseoligonucleotides which are covalently linked to organic moieties, suchas those described in WO 90/10048, and other moieties that increasesaffinity of the oligonucleotide for a target nucleic acid sequence, suchas poly-(L-lysine). Further still, intercalating agents, such asellipticine, and alkylating agents or metal complexes may be attached tosense or antisense oligonucleotides to modify binding specificities ofthe antisense or sense oligonucleotide for the target nucleotidesequence.

Antisense or sense oligonucleotides may be introduced into a cellcontaining the target nucleic acid sequence by any gene transfer method,including, for example, CaPO₄-mediated DNA transfection,electroporation, or by using gene transfer vectors such as Epstein-Barrvirus. In a preferred procedure, an antisense or sense oligonucleotideis inserted into a suitable retroviral vector. A cell containing thetarget nucleic acid sequence is contacted with the recombinantretroviral vector, either in vivo or ex vivo. Suitable retroviralvectors include, but are not limited to, those derived from the murineretrovirus M-MuLV, N2 (a retrovirus derived from M-MuLV), or the doublecopy vectors designated DCT5A, DCT5B and DCT5C (see WO 90/13641).

Sense or antisense oligonucleotides also may be introduced into a cellcontaining the target nucleotide sequence by formation of a conjugatewith a ligand binding molecule, as described in WO 91/04753. Suitableligand binding molecules include, but are not limited to, cell surfacereceptors, growth factors, other cytokines, or other ligands that bindto cell surface receptors. Preferably, conjugation of the ligand bindingmolecule does not substantially interfere with the ability of the ligandbinding molecule to bind to its corresponding molecule or receptor, orblock entry of the sense or antisense oligonucleotide or its conjugatedversion into the cell.

Alternatively, a sense or an antisense oligonucleotide may be introducedinto a cell containing the target nucleic acid sequence by formation ofan oligonucleotide-lipid complex, as described in WO 90/10448. The senseor antisense oligonucleotide-lipid complex is preferably dissociatedwithin the cell by an endogenous lipase.

Antisense or sense RNA or DNA molecules are generally at least about 5nucleotides in length, alternatively at least about 6, 7, 8, 9, 10, 11,12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29,30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 105, 110,115, 120, 125, 130, 135, 140, 145, 150, 155, 160, 165, 170, 175, 180,185, 190, 195, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300,310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440,450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580,590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720,730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860,870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, or 1000nucleotides in length, wherein in this context the term “about” meansthe referenced nucleotide sequence length plus or minus 10% of thatreferenced length.

The probes may also be employed in PCR techniques to generate a pool ofsequences for identification of closely related TAT coding sequences.

Nucleotide sequences encoding a TAT can also be used to constructhybridization probes for mapping the gene which encodes that TAT and forthe genetic analysis of individuals with genetic disorders. Thenucleotide sequences provided herein may be mapped to a chromosome andspecific regions of a chromosome using known techniques, such as in situhybridization, linkage analysis against known chromosomal markers, andhybridization screening with libraries.

When the coding sequences for TAT encode a protein which binds toanother protein (example, where the TAT is a receptor), the TAT can beused in assays to identify the other proteins or molecules involved inthe binding interaction. By such methods, inhibitors of thereceptor/ligand binding interaction can be identified. Proteins involvedin such binding interactions can also be used to screen for peptide orsmall molecule inhibitors or agonists of the binding interaction. Also,the receptor TAT can be used to isolate correlative ligand(s). Screeningassays can be designed to find lead compounds that mimic the biologicalactivity of a native TAT or a receptor for TAT. Such screening assayswill include assays amenable to high-throughput screening of chemicallibraries, making them particularly suitable for identifying smallmolecule drug candidates. Small molecules contemplated include syntheticorganic or inorganic compounds. The assays can be performed in a varietyof formats, including protein-protein binding assays, biochemicalscreening assays, immunoassays and cell based assays, which are wellcharacterized in the art.

Nucleic acids which encode TAT or its modified forms can also be used togenerate either transgenic animals or “knock out” animals which, inturn, are useful in the development and screening of therapeuticallyuseful reagents. A transgenic animal (e.g., a mouse or rat) is an animalhaving cells that contain a transgene, which transgene was introducedinto the animal or an ancestor of the animal at a prenatal, e.g., anembryonic stage. A transgene is a DNA which is integrated into thegenome of a cell from which a transgenic animal develops. In oneembodiment, cDNA encoding TAT can be used to clone genomic DNA encodingTAT in accordance with established techniques and the genomic sequencesused to generate transgenic animals that contain cells which express DNAencoding TAT. Methods for generating transgenic animals, particularlyanimals such as mice or rats, have become conventional in the art andare described, for example, in U.S. Pat. Nos. 4,736,866 and 4,870,009.Typically, particular cells would be targeted for TAT transgeneincorporation with tissue-specific enhancers. Transgenic animals thatinclude a copy of a transgene encoding TAT introduced into the germ lineof the animal at an embryonic stage can be used to examine the effect ofincreased expression of DNA encoding TAT. Such animals can be used astester animals for reagents thought to confer protection from, forexample, pathological conditions associated with its overexpression. Inaccordance with this facet of the invention, an animal is treated withthe reagent and a reduced incidence of the pathological condition,compared to untreated animals bearing the transgene, would indicate apotential therapeutic intervention for the pathological condition.

Alternatively, non-human homologues of TAT can be used to construct aTAT “knock out” animal which has a defective or altered gene encodingTAT as a result of homologous recombination between the endogenous geneencoding TAT and altered genomic DNA encoding TAT introduced into anembryonic stem cell of the animal. For example, cDNA encoding TAT can beused to clone genomic DNA encoding TAT in accordance with establishedtechniques. A portion of the genomic DNA encoding TAT can be deleted orreplaced with another gene, such as a gene encoding a selectable markerwhich can be used to monitor integration. Typically, several kilobasesof unaltered flanking DNA (both at the 5′ and 3′ ends) are included inthe vector [see e.g., Thomas and Capecchi, Cell, 51:503 (1987) for adescription of homologous recombination vectors]. The vector isintroduced into an embryonic stem cell line (e.g., by electroporation)and cells in which the introduced DNA has homologously recombined withthe endogenous DNA are selected [see e.g., Li et al., Cell, 69:915(1992)]. The selected cells are then injected into a blastocyst of ananimal (e.g., a mouse or rat) to form aggregation chimeras [see e.g.,Bradley, in Teratocarcinomas and Embryonic Stem Cells: A PracticalApproach, E. J. Robertson, ed. (IRL, Oxford, 1987), pp. 113-152]. Achimeric embryo can then be implanted into a suitable pseudopregnantfemale foster animal and the embryo brought to term to create a “knockout” animal. Progeny harboring the homologously recombined DNA in theirgerm cells can be identified by standard techniques and used to breedanimals in which all cells of the animal contain the homologouslyrecombined DNA. Knockout animals can be characterized for instance, fortheir ability to defend against certain pathological conditions and fortheir development of pathological conditions due to absence of the TATpolypeptide.

Nucleic acid encoding the TAT polypeptides may also be used in genetherapy. In gene therapy applications, genes are introduced into cellsin order to achieve in vivo synthesis of a therapeutically effectivegenetic product, for example for replacement of a defective gene. “Genetherapy” includes both conventional gene therapy where a lasting effectis achieved by a single treatment, and the administration of genetherapeutic agents, which involves the one time or repeatedadministration of a therapeutically effective DNA or mRNA. AntisenseRNAs and DNAs can be used as therapeutic agents for blocking theexpression of certain genes in vivo. It has already been shown thatshort antisense oligonucleotides can be imported into cells where theyact as inhibitors, despite their low intracellular concentrations causedby their restricted uptake by the cell membrane. (Zamecnik et al., Proc.Natl. Acad. Sci. USA 83:4143-4146 [1986]). The oligonucleotides can bemodified to enhance their uptake, e.g. by substituting their negativelycharged phosphodiester groups by uncharged groups.

There are a variety of techniques available for introducing nucleicacids into viable cells. The techniques vary depending upon whether thenucleic acid is transferred into cultured cells in vitro, or in vivo inthe cells of the intended host. Techniques suitable for the transfer ofnucleic acid into mammalian cells in vitro include the use of liposomes,electroporation, microinjection, cell fusion, DEAE-dextran, the calciumphosphate precipitation method, etc. The currently preferred in vivogene transfer techniques include transfection with viral (typicallyretroviral) vectors and viral coat protein-liposome mediatedtransfection (Dzau et al., Trends in Biotechnology 11, 205-210 [1993]).In some situations it is desirable to provide the nucleic acid sourcewith an agent that targets the target cells, such as an antibodyspecific for a cell surface membrane protein or the target cell, aligand for a receptor on the target cell, etc. Where liposomes areemployed, proteins which bind to a cell surface membrane proteinassociated with endocytosis may be used for targeting and/or tofacilitate uptake, e.g. capsid proteins or fragments thereof tropic fora particular cell type, antibodies for proteins which undergointernalization in cycling, proteins that target intracellularlocalization and enhance intracellular half-life. The technique ofreceptor-mediated endocytosis is described, for example, by Wu et al.,J. Biol. Chem. 262, 4429-4432 (1987); and Wagner et al., Proc. Natl.Acad. Sci. USA 87, 3410-3414 (1990). For review of gene marking and genetherapy protocols see Anderson et al., Science 256, 808-813 (1992).

The nucleic acid molecules encoding the TAT polypeptides or fragmentsthereof described herein are useful for chromosome identification. Inthis regard, there exists an ongoing need to identify new chromosomemarkers, since relatively few chromosome marking reagents, based uponactual sequence data are presently available. Each TAT nucleic acidmolecule of the present invention can be used as a chromosome marker.

The TAT polypeptides and nucleic acid molecules of the present inventionmay also be used diagnostically for tissue typing, wherein the TATpolypeptides of the present invention may be differentially expressed inone tissue as compared to another, preferably in a diseased tissue ascompared to a normal tissue of the same tissue type. TAT nucleic acidmolecules will find use for generating probes for PCR, Northernanalysis, Southern analysis and Western analysis.

This invention encompasses methods of screening compounds to identifythose that mimic the TAT polypeptide (agonists) or prevent the effect ofthe TAT polypeptide (antagonists). Screening assays for antagonist drugcandidates are designed to identify compounds that bind or complex withthe TAT polypeptides encoded by the genes identified herein, orotherwise interfere with the interaction of the encoded polypeptideswith other cellular proteins, including e.g., inhibiting the expressionof TAT polypeptide from cells. Such screening assays will include assaysamenable to high-throughput screening of chemical libraries, making themparticularly suitable for identifying small molecule drug candidates.

The assays can be performed in a variety of formats, includingprotein-protein binding assays, biochemical screening assays,immunoassays, and cell-based assays, which are well characterized in theart.

All assays for antagonists are common in that they call for contactingthe drug candidate with a TAT polypeptide encoded by a nucleic acididentified herein under conditions and for a time sufficient to allowthese two components to interact.

In binding assays, the interaction is binding and the complex formed canbe isolated or detected in the reaction mixture. In a particularembodiment, the TAT polypeptide encoded by the gene identified herein orthe drug candidate is immobilized on a solid phase, e.g., on amicrotiter plate, by covalent or non-covalent attachments. Non-covalentattachment generally is accomplished by coating the solid surface with asolution of the TAT polypeptide and drying. Alternatively, animmobilized antibody, e.g., a monoclonal antibody, specific for the TATpolypeptide to be immobilized can be used to anchor it to a solidsurface. The assay is performed by adding the non-immobilized component,which may be labeled by a detectable label, to the immobilizedcomponent, e.g., the coated surface containing the anchored component.When the reaction is complete, the non-reacted components are removed,e.g., by washing, and complexes anchored on the solid surface aredetected. When the originally non-immobilized component carries adetectable label, the detection of label immobilized on the surfaceindicates that complexing occurred. Where the originally non-immobilizedcomponent does not carry a label, complexing can be detected, forexample, by using a labeled antibody specifically binding theimmobilized complex.

If the candidate compound interacts with but does not bind to aparticular TAT polypeptide encoded by a gene identified herein, itsinteraction with that polypeptide can be assayed by methods well knownfor detecting protein-protein interactions. Such assays includetraditional approaches, such as, e.g., cross-linking,co-immunoprecipitation, and co-purification through gradients orchromatographic columns. In addition, protein-protein interactions canbe monitored by using a yeast-based genetic system described by Fieldsand co-workers (Fields and Song, Nature (London), 340:245-246 (1989);Chien et al., Proc. Natl. Acad. Sci. USA, 88:9578-9582 (1991)) asdisclosed by Chevray and Nathans, Proc. Natl. Acad. Sci. USA, 89:5789-5793 (1991). Many transcriptional activators, such as yeast GAL4,consist of two physically discrete modular domains, one acting as theDNA-binding domain, the other one functioning as thetranscription-activation domain. The yeast expression system describedin the foregoing publications (generally referred to as the “two-hybridsystem”) takes advantage of this property, and employs two hybridproteins, one in which the target protein is fused to the DNA-bindingdomain of GAL4, and another, in which candidate activating proteins arefused to the activation domain. The expression of a GAL1-lacZ reportergene under control of a GAL4-activated promoter depends onreconstitution of GAL4 activity via protein-protein interaction.Colonies containing interacting polypeptides are detected with achromogenic substrate for β-galactosidase. A complete kit (MATCHMAKER™)for identifying protein-protein interactions between two specificproteins using the two-hybrid technique is commercially available fromClontech. This system can also be extended to map protein domainsinvolved in specific protein interactions as well as to pinpoint aminoacid residues that are crucial for these interactions.

Compounds that interfere with the interaction of a gene encoding a TATpolypeptide identified herein and other intra- or extracellularcomponents can be tested as follows: usually a reaction mixture isprepared containing the product of the gene and the intra- orextracellular component under conditions and for a time allowing for theinteraction and binding of the two products. To test the ability of acandidate compound to inhibit binding, the reaction is run in theabsence and in the presence of the test compound. In addition, a placebomay be added to a third reaction mixture, to serve as positive control.The binding (complex formation) between the test compound and the intra-or extracellular component present in the mixture is monitored asdescribed hereinabove. The formation of a complex in the controlreaction(s) but not in the reaction mixture containing the test compoundindicates that the test compound interferes with the interaction of thetest compound and its reaction partner.

To assay for antagonists, the TAT polypeptide may be added to a cellalong with the compound to be screened for a particular activity and theability of the compound to inhibit the activity of interest in thepresence of the TAT polypeptide indicates that the compound is anantagonist to the TAT polypeptide. Alternatively, antagonists may bedetected by combining the TAT polypeptide and a potential antagonistwith membrane-bound TAT polypeptide receptors or recombinant receptorsunder appropriate conditions for a competitive inhibition assay. The TATpolypeptide can be labeled, such as by radioactivity, such that thenumber of TAT polypeptide molecules bound to the receptor can be used todetermine the effectiveness of the potential antagonist. The geneencoding the receptor can be identified by numerous methods known tothose of skill in the art, for example, ligand panning and FACS sorting.Coligan et al., Current Protocols in Immun., 1(2): Chapter 5 (1991).Preferably, expression cloning is employed wherein polyadenylated RNA isprepared from a cell responsive to the TAT polypeptide and a cDNAlibrary created from this RNA is divided into pools and used totransfect COS cells or other cells that are not responsive to the TATpolypeptide. Transfected cells that are grown on glass slides areexposed to labeled TAT polypeptide. The TAT polypeptide can be labeledby a variety of means including iodination or inclusion of a recognitionsite for a site-specific protein kinase. Following fixation andincubation, the slides are subjected to autoradiographic analysis.Positive pools are identified and sub-pools are prepared andre-transfected using an interactive sub-pooling and re-screeningprocess, eventually yielding a single clone that encodes the putativereceptor.

As an alternative approach for receptor identification, labeled TATpolypeptide can be photoaffinity-linked with cell membrane or extractpreparations that express the receptor molecule. Cross-linked materialis resolved by PAGE and exposed to X-ray film. The labeled complexcontaining the receptor can be excised, resolved into peptide fragments,and subjected to protein micro-sequencing. The amino acid sequenceobtained from micro-sequencing would be used to design a set ofdegenerate oligonucleotide probes to screen a cDNA library to identifythe gene encoding the putative receptor.

In another assay for antagonists, mammalian cells or a membranepreparation expressing the receptor would be incubated with labeled TATpolypeptide in the presence of the candidate compound. The ability ofthe compound to enhance or block this interaction could then bemeasured.

More specific examples of potential antagonists include anoligonucleotide that binds to the fusions of immunoglobulin with TATpolypeptide, and, in particular, antibodies including, withoutlimitation, poly- and monoclonal antibodies and antibody fragments,single-chain antibodies, anti-idiotypic antibodies, and chimeric orhumanized versions of such antibodies or fragments, as well as humanantibodies and antibody fragments. Alternatively, a potential antagonistmay be a closely related protein, for example, a mutated form of the TATpolypeptide that recognizes the receptor but imparts no effect, therebycompetitively inhibiting the action of the TAT polypeptide.

Another potential TAT polypeptide antagonist is an antisense RNA or DNAconstruct prepared using antisense technology, where, e.g., an antisenseRNA or DNA molecule acts to block directly the translation of mRNA byhybridizing to targeted mRNA and preventing protein translation.Antisense technology can be used to control gene expression throughtriple-helix formation or antisense DNA or RNA, both of which methodsare based on binding of a polynucleotide to DNA or RNA. For example, the5′ coding portion of the polynucleotide sequence, which encodes themature TAT polypeptides herein, is used to design an antisense RNAoligonucleotide of from about 10 to 40 base pairs in length. A DNAoligonucleotide is designed to be complementary to a region of the geneinvolved in transcription (triple helix—see Lee et al., Nucl. AcidsRes., 6:3073 (1979); Cooney et al., Science, 241: 456 (1988); Dervan etal., Science, 251:1360 (1991)), thereby preventing transcription and theproduction of the TAT polypeptide. The antisense RNA oligonucleotidehybridizes to the mRNA in vivo and blocks translation of the mRNAmolecule into the TAT polypeptide (antisense—Okano, Neurochem., 56:560(1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression(CRC Press: Boca Raton, Fla., 1988). The oligonucleotides describedabove can also be delivered to cells such that the antisense RNA or DNAmay be expressed in vivo to inhibit production of the TAT polypeptide.When antisense DNA is used, oligodeoxyribonucleotides derived from thetranslation-initiation site, e.g., between about −10 and +10 positionsof the target gene nucleotide sequence, are preferred.

Potential antagonists include small molecules that bind to the activesite, the receptor binding site, or growth factor or other relevantbinding site of the TAT polypeptide, thereby blocking the normalbiological activity of the TAT polypeptide. Examples of small moleculesinclude, but are not limited to, small peptides or peptide-likemolecules, preferably soluble peptides, and synthetic non-peptidylorganic or inorganic compounds.

Ribozymes are enzymatic RNA molecules capable of catalyzing the specificcleavage of RNA. Ribozymes act by sequence-specific hybridization to thecomplementary target RNA, followed by endonucleolytic cleavage. Specificribozyme cleavage sites within a potential RNA target can be identifiedby known techniques. For further details see, e.g., Rossi, CurrentBiology, 4:469-471 (1994), and PCT publication No. WO 97/33551(published Sep. 18, 1997).

Nucleic acid molecules in triple-helix formation used to inhibittranscription should be single-stranded and composed ofdeoxynucleotides. The base composition of these oligonucleotides isdesigned such that it promotes triple-helix formation via Hoogsteenbase-pairing rules, which generally require sizeable stretches ofpurines or pyrimidines on one strand of a duplex. For further detailssee, e.g., PCT publication No. WO 97/33551, supra.

These small molecules can be identified by any one or more of thescreening assays discussed hereinabove and/or by any other screeningtechniques well known for those skilled in the art.

Isolated TAT polypeptide-encoding nucleic acid can be used herein forrecombinantly producing TAT polypeptide using techniques well known inthe art and as described herein. In turn, the produced TAT polypeptidescan be employed for generating anti-TAT antibodies using techniques wellknown in the art and as described herein.

Antibodies specifically binding a TAT polypeptide identified herein, aswell as other molecules identified by the screening assays disclosedhereinbefore, can be administered for the treatment of variousdisorders, including cancer, in the form of pharmaceutical compositions.

If the TAT polypeptide is intracellular and whole antibodies are used asinhibitors, internalizing antibodies are preferred. However,lipofections or liposomes can also be used to deliver the antibody, oran antibody fragment, into cells. Where antibody fragments are used, thesmallest inhibitory fragment that specifically binds to the bindingdomain of the target protein is preferred. For example, based upon thevariable-region sequences of an antibody, peptide molecules can bedesigned that retain the ability to bind the target protein sequence.Such peptides can be synthesized chemically and/or produced byrecombinant DNA technology. See, e.g., Marasco et al., Proc. Natl. Acad.Sci. USA, 90: 7889-7893 (1993).

The formulation herein may also contain more than one active compound asnecessary for the particular indication being treated, preferably thosewith complementary activities that do not adversely affect each other.Alternatively, or in addition, the composition may comprise an agentthat enhances its function, such as, for example, a cytotoxic agent,cytokine, chemotherapeutic agent, or growth-inhibitory agent. Suchmolecules are suitably present in combination in amounts that areeffective for the purpose intended.

The following examples are offered for illustrative purposes only, andare not intended to limit the scope of the present invention in any way.

All patent and literature references cited in the present specificationare hereby incorporated by reference in their entirety.

EXAMPLES

Commercially available reagents referred to in the examples were usedaccording to manufacturer's instructions unless otherwise indicated. Thesource of those cells identified in the following examples, andthroughout the specification, by ATCC accession numbers is the AmericanType Culture Collection, Manassas, Va.

Example 1 Tissue Expression Profiling Using GeneExpress®

A proprietary database containing gene expression information(GeneExpress®, Gene Logic Inc., Gaithersburg, Md.) was analyzed in anattempt to identify polypeptides (and their encoding nucleic acids)whose expression is significantly upregulated in a particular tumortissue(s) of interest as compared to other tumor(s) and/or normaltissues. Specifically, analysis of the GeneExpress® database wasconducted using either software available through Gene Logic Inc.,Gaithersburg, Md., for use with the GeneExpress® database or withproprietary software written and developed at Genentech, Inc. for usewith the GeneExpress® database. The rating of positive hits in theanalysis is based upon several criteria including, for example, tissuespecificity, tumor specificity and expression level in normal essentialand/or normal proliferating tissues. The following is a list ofmolecules whose tissue expression profile as determined from an analysisof the GeneExpress® database evidences high tissue expression andsignificant upregulation of expression in a specific tumor or tumors ascompared to other tumor(s) and/or normal tissues and optionallyrelatively low expression in normal essential and/or normalproliferating tissues. As such, the molecules listed below are excellentpolypeptide targets for the diagnosis and therapy of cancer in mammals.

upregulation of Molecule expression in: as compared to: DNA45234-1277(TAT291) breast tumor normal breast tissue DNA45234-1277 (TAT291) ovarytumor normal ovary tissue DNA45234-1277 (TAT291) uterus tumor normaluterus tissue DNA37151-1193 (TAT292) breast tumor normal breast tissueDNA37151-1193 (TAT292) fallopian tube tumor normal fallopian tube tissueDNA37151-1193 (TAT292) ovary tumor normal ovary tissue DNA37151-1193(TAT292) uterus tumor normal uterus tissue

Example 2 Microarray Analysis to Detect Upregulation of TAT Polypeptidesin Cancerous Tumors

Nucleic acid microarrays, often containing thousands of gene sequences,are useful for identifying differentially expressed genes in diseasedtissues as compared to their normal counterparts. Using nucleic acidmicroarrays, test and control mRNA samples from test and control tissuesamples are reverse transcribed and labeled to generate cDNA probes. ThecDNA probes are then hybridized to an array of nucleic acids immobilizedon a solid support. The array is configured such that the sequence andposition of each member of the array is known. For example, a selectionof genes known to be expressed in certain disease states may be arrayedon a solid support. Hybridization of a labeled probe with a particulararray member indicates that the sample from which the probe was derivedexpresses that gene. If the hybridization signal of a probe from a test(disease tissue) sample is greater than hybridization signal of a probefrom a control (normal tissue) sample, the gene or genes overexpressedin the disease tissue are identified. The implication of this result isthat an overexpressed protein in a diseased tissue is useful not only asa diagnostic marker for the presence of the disease condition, but alsoas a therapeutic target for treatment of the disease condition.

The methodology of hybridization of nucleic acids and microarraytechnology is well known in the art. In one example, the specificpreparation of nucleic acids for hybridization and probes, slides, andhybridization conditions are all detailed in PCT Patent ApplicationSerial No. PCT/US01/10482, filed on Mar. 30, 2001 and which is hereinincorporated by reference.

In the present example, cancerous tumors derived from various humantissues were studied for upregulated gene expression relative tocancerous tumors from different tissue types and/or non-cancerous humantissues in an attempt to identify those polypeptides which areoverexpressed in a particular cancerous tumor(s). In certainexperiments, cancerous human tumor tissue and non-cancerous human tumortissue of the same tissue type (often from the same patient) wereobtained and analyzed for TAT polypeptide expression. Additionally,cancerous human tumor tissue from any of a variety of different humantumors was obtained and compared to a “universal” epithelial controlsample which was prepared by pooling non-cancerous human tissues ofepithelial origin, including liver, kidney, and lung. mRNA isolated fromthe pooled tissues represents a mixture of expressed gene products fromthese different tissues. Microarray hybridization experiments using thepooled control samples generated a linear plot in a 2-color analysis.The slope of the line generated in a 2-color analysis was then used tonormalize the ratios of (test:control detection) within each experiment.The normalized ratios from various experiments were then compared andused to identify clustering of gene expression. Thus, the pooled“universal control” sample not only allowed effective relative geneexpression determinations in a simple 2-sample comparison, it alsoallowed multi-sample comparisons across several experiments.

In the present experiments, nucleic acid probes derived from the hereindescribed TAT polypeptide-encoding nucleic acid sequences were used inthe creation of the microarray and RNA from various tumor tissues wereused for the hybridization thereto. Below is shown the results of theseexperiments, demonstrating that various TAT polypeptides of the presentinvention are significantly overexpressed in various human tumor tissuesas compared to other human tumor tissues and/or non-cancerous humantissue(s). As described above, these data demonstrate that the TATpolypeptides of the present invention are useful not only as diagnosticmarkers for the presence of one or more cancerous tumors, but also serveas therapeutic targets for the treatment of those tumors.

upregulation of Molecule expression in: as compared to: DNA45234-1277(TAT291) breast tumor normal breast tissue epithelial control

Example 3 Verification of Differential TAT Polypeptide Expression byGEPIS

TAT polypeptides which may have been identified as a tumor antigen asdescribed in one or more of the above Examples were analyzed andverified as follows. An expressed sequence tag (EST) DNA database(LIFESEQ®, Incyte Pharmaceuticals, Palo Alto, Calif.) was searched andinteresting EST sequences were identified by GEPIS. Gene expressionprofiling in silico (GEPIS) is a bioinformatics tool developed atGenentech, Inc. that characterizes genes of interest for new cancertherapeutic targets. GEPIS takes advantage of large amounts of ESTsequence and library information to determine gene expression profiles.GEPIS is capable of determining the expression profile of a gene basedupon its proportional correlation with the number of its occurrences inEST databases, and it works by integrating the LIFESEQ® EST relationaldatabase and Genentech proprietary information in a stringent andstatistically meaningful way. In this example, GEPIS is used to identifyand cross-validate novel tumor antigens, although GEPIS can beconfigured to perform either very specific analyses or broad screeningtasks. For the initial screen, GEPIS is used to identify EST sequencesfrom the LIFESEQ® database that correlate to expression in a particulartissue or tissues of interest (often a tumor tissue of interest). TheEST sequences identified in this initial screen (or consensus sequencesobtained from aligning multiple related and overlapping EST sequencesobtained from the initial screen) were then subjected to a screenintended to identify the presence of at least one transmembrane domainin the encoded protein. Finally, GEPIS was employed to generate acomplete tissue expression profile for the various sequences ofinterest. Using this type of screening bioinformatics, various TATpolypeptides (and their encoding nucleic acid molecules) were identifiedas being significantly overexpressed in a particular type of cancer orcertain cancers as compared to other cancers and/or normal non-canceroustissues. The rating of GEPIS hits is based upon several criteriaincluding, for example, tissue specificity, tumor specificity andexpression level in normal essential and/or normal proliferatingtissues. The following is a list of molecules whose tissue expressionprofile as determined by GEPIS evidences high tissue expression andsignificant upregulation of expression in a specific tumor or tumors ascompared to other tumor(s) and/or normal tissues and optionallyrelatively low expression in normal essential and/or normalproliferating tissues. As such, the molecules listed below are excellentpolypeptide targets for the diagnosis and therapy of cancer in mammals.

upregulation of Molecule expression in: as compared to: DNA45234-1277(TAT291) breast tumor normal breast tissue DNA45234-1277 (TAT291) ovarytumor normal ovary tissue DNA45234-1277 (TAT291) uterus tumor normaluterus tissue DNA37151-1193 (TAT292) breast tumor normal breast tissueDNA37151-1193 (TAT292) fallopian tube tumor normal fallopian tube tissueDNA37151-1193 (TAT292) ovary tumor normal ovary tissue DNA37151-1193(TAT292) uterus tumor normal uterus tissue

Example 4 Use of TAT as a Hybridization Probe

The following method describes use of a nucleotide sequence encoding TATas a hybridization probe for, i.e., diagnosis of the presence of a tumorin a mammal.

DNA comprising the coding sequence of full-length or mature TAT asdisclosed herein can also be employed as a probe to screen forhomologous DNAs (such as those encoding naturally-occurring variants ofTAT) in human tissue cDNA libraries or human tissue genomic libraries.

Hybridization and washing of filters containing either library DNAs isperformed under the following high stringency conditions. Hybridizationof radiolabeled TAT-derived probe to the filters is performed in asolution of 50% formamide, 5×SSC, 0.1% SDS, 0.1% sodium pyrophosphate,50 mM sodium phosphate, pH 6.8, 2×Denhardt's solution, and 10% dextransulfate at 42° C. for 20 hours. Washing of the filters is performed inan aqueous solution of 0.1×SSC and 0.1% SDS at 42° C.

DNAs having a desired sequence identity with the DNA encodingfull-length native sequence TAT can then be identified using standardtechniques known in the art.

Example 5 Expression of TAT in E. coli

This example illustrates preparation of an unglycosylated form of TAT byrecombinant expression in E. coli.

The DNA sequence encoding TAT is initially amplified using selected PCRprimers. The primers should contain restriction enzyme sites whichcorrespond to the restriction enzyme sites on the selected expressionvector. A variety of expression vectors may be employed. An example of asuitable vector is pBR322 (derived from E. coli; see Bolivar et al.,Gene, 2:95 (1977)) which contains genes for ampicillin and tetracyclineresistance. The vector is digested with restriction enzyme anddephosphorylated. The PCR amplified sequences are then ligated into thevector. The vector will preferably include sequences which encode for anantibiotic resistance gene, a trp promoter, a polyhis leader (includingthe first six STII codons, polyhis sequence, and enterokinase cleavagesite), the TAT coding region, lambda transcriptional terminator, and anargU gene.

The ligation mixture is then used to transform a selected E. coli strainusing the methods described in Sambrook et al., supra. Transformants areidentified by their ability to grow on LB plates and antibioticresistant colonies are then selected. Plasmid DNA can be isolated andconfirmed by restriction analysis and DNA sequencing.

Selected clones can be grown overnight in liquid culture medium such asLB broth supplemented with antibiotics. The overnight culture maysubsequently be used to inoculate a larger scale culture. The cells arethen grown to a desired optical density, during which the expressionpromoter is turned on.

After culturing the cells for several more hours, the cells can beharvested by centrifugation. The cell pellet obtained by thecentrifugation can be solubilized using various agents known in the art,and the solubilized TAT protein can then be purified using a metalchelating column under conditions that allow tight binding of theprotein.

TAT may be expressed in E. coli in a poly-His tagged form, using thefollowing procedure. The DNA encoding TAT is initially amplified usingselected PCR primers. The primers will contain restriction enzyme siteswhich correspond to the restriction enzyme sites on the selectedexpression vector, and other useful sequences providing for efficientand reliable translation initiation, rapid purification on a metalchelation column, and proteolytic removal with enterokinase. ThePCR-amplified, poly-His tagged sequences are then ligated into anexpression vector, which is used to transform an E. coli host based onstrain 52 (W3110 fuhA(tonA) Ion gale rpoHts(htpRts) clpP(lacIq).Transformants are first grown in LB containing 50 mg/ml carbenicillin at30° C. with shaking until an O.D. 600 of 3-5 is reached. Cultures arethen diluted 50-100 fold into CRAP media (prepared by mixing 3.57 g(NH₄)₂SO₄, 0.71 g sodium citrate 2H2O, 1.07 g KCl, 5.36 g Difco yeastextract, 5.36 g Sheffield hycase SF in 500 mL water, as well as 110 mMMPOS, pH 7.3, 0.55% (w/v) glucose and 7 mM MgSO₄) and grown forapproximately 20-30 hours at 30° C. with shaking. Samples are removed toverify expression by SDS-PAGE analysis, and the bulk culture iscentrifuged to pellet the cells. Cell pellets are frozen untilpurification and refolding.

E. coli paste from 0.5 to 1 L fermentations (6-10 g pellets) isresuspended in 10 volumes (w/v) in 7 M guanidine, 20 mM Tris, pH 8buffer. Solid sodium sulfite and sodium tetrathionate is added to makefinal concentrations of 0.1 M and 0.02 M, respectively, and the solutionis stirred overnight at 4° C. This step results in a denatured proteinwith all cysteine residues blocked by sulfitolization. The solution iscentrifuged at 40,000 rpm in a Beckman Ultracentifuge for 30 min. Thesupernatant is diluted with 3-5 volumes of metal chelate column buffer(6 M guanidine, 20 mM Tris, pH 7.4) and filtered through 0.22 micronfilters to clarify. The clarified extract is loaded onto a 5 ml QiagenNi-NTA metal chelate column equilibrated in the metal chelate columnbuffer. The column is washed with additional buffer containing 50 mMimidazole (Calbiochem, Utrol grade), pH 7.4. The protein is eluted withbuffer containing 250 mM imidazole. Fractions containing the desiredprotein are pooled and stored at 4° C. Protein concentration isestimated by its absorbance at 280 nm using the calculated extinctioncoefficient based on its amino acid sequence.

The proteins are refolded by diluting the sample slowly into freshlyprepared refolding buffer consisting of: 20 mM Tris, pH 8.6, 0.3 M NaCl,2.5 M urea, 5 mM cysteine, 20 mM glycine and 1 mM EDTA. Refoldingvolumes are chosen so that the final protein concentration is between 50to 100 micrograms/ml. The refolding solution is stirred gently at 4° C.for 12-36 hours. The refolding reaction is quenched by the addition ofTFA to a final concentration of 0.4% (pH of approximately 3). Beforefurther purification of the protein, the solution is filtered through a0.22 micron filter and acetonitrile is added to 2-10% finalconcentration. The refolded protein is chromatographed on a Poros R1/Hreversed phase column using a mobile buffer of 0.1% TFA with elutionwith a gradient of acetonitrile from 10 to 80%. Aliquots of fractionswith A280 absorbance are analyzed on SDS polyacrylamide gels andfractions containing homogeneous refolded protein are pooled. Generally,the properly refolded species of most proteins are eluted at the lowestconcentrations of acetonitrile since those species are the most compactwith their hydrophobic interiors shielded from interaction with thereversed phase resin. Aggregated species are usually eluted at higheracetonitrile concentrations. In addition to resolving misfolded forms ofproteins from the desired form, the reversed phase step also removesendotoxin from the samples.

Fractions containing the desired folded TAT polypeptide are pooled andthe acetonitrile removed using a gentle stream of nitrogen directed atthe solution. Proteins are formulated into 20 mM Hepes, pH 6.8 with 0.14M sodium chloride and 4% mannitol by dialysis or by gel filtration usingG25 Superfine (Pharmacia) resins equilibrated in the formulation bufferand sterile filtered.

Certain of the TAT polypeptides disclosed herein have been successfullyexpressed and purified using this technique(s).

Example 6 Expression of TAT in Mammalian Cells

This example illustrates preparation of a potentially glycosylated formof TAT by recombinant expression in mammalian cells.

The vector, pRK5 (see EP 307,247, published Mar. 15, 1989), is employedas the expression vector. Optionally, the TAT DNA is ligated into pRK5with selected restriction enzymes to allow insertion of the TAT DNAusing ligation methods such as described in Sambrook et al., supra. Theresulting vector is called pRK5-TAT.

In one embodiment, the selected host cells may be 293 cells. Human 293cells (ATCC CCL 1573) are grown to confluence in tissue culture platesin medium such as DMEM supplemented with fetal calf serum andoptionally, nutrient components and/or antibiotics. About 10 μg pRK5-TATDNA is mixed with about 1 μg DNA encoding the VA RNA gene [Thimmappayaet al., Cell, 31:543 (1982)] and dissolved in 500 μl of 1 mM Tris-HCl,0.1 mM EDTA, 0.227 M CaCl₂. To this mixture is added, dropwise, 500 μlof 50 mM HEPES (pH 7.35), 280 mM NaCl, 1.5 mM NaPO₄, and a precipitateis allowed to form for 10 minutes at 25° C. The precipitate is suspendedand added to the 293 cells and allowed to settle for about four hours at37° C. The culture medium is aspirated off and 2 ml of 20% glycerol inPBS is added for 30 seconds. The 293 cells are then washed with serumfree medium, fresh medium is added and the cells are incubated for about5 days.

Approximately 24 hours after the transfections, the culture medium isremoved and replaced with culture medium (alone) or culture mediumcontaining 200 μCi/ml ³⁵S-cysteine and 200 μCi/ml ³⁵S-methionine. Aftera 12 hour incubation, the conditioned medium is collected, concentratedon a spin filter, and loaded onto a 15% SDS gel. The processed gel maybe dried and exposed to film for a selected period of time to reveal thepresence of TAT polypeptide. The cultures containing transfected cellsmay undergo further incubation (in serum free medium) and the medium istested in selected bioassays.

In an alternative technique, TAT may be introduced into 293 cellstransiently using the dextran sulfate method described by Somparyrac etal., Proc. Natl. Acad. Sci., 12:7575 (1981). 293 cells are grown tomaximal density in a spinner flask and 700 μg pRK5-TAT DNA is added. Thecells are first concentrated from the spinner flask by centrifugationand washed with PBS. The DNA-dextran precipitate is incubated on thecell pellet for four hours. The cells are treated with 20% glycerol for90 seconds, washed with tissue culture medium, and re-introduced intothe spinner flask containing tissue culture medium, 5 μg/ml bovineinsulin and 0.1 μg/ml bovine transferrin. After about four days, theconditioned media is centrifuged and filtered to remove cells anddebris. The sample containing expressed TAT can then be concentrated andpurified by any selected method, such as dialysis and/or columnchromatography.

In another embodiment, TAT can be expressed in CHO cells. The pRK5-TATcan be transfected into CHO cells using known reagents such as CaPO₄ orDEAE-dextran. As described above, the cell cultures can be incubated,and the medium replaced with culture medium (alone) or medium containinga radiolabel such as ³⁵S-methionine. After determining the presence ofTAT polypeptide, the culture medium may be replaced with serum freemedium. Preferably, the cultures are incubated for about 6 days, andthen the conditioned medium is harvested. The medium containing theexpressed TAT can then be concentrated and purified by any selectedmethod.

Epitope-tagged TAT may also be expressed in host CHO cells. The TAT maybe subcloned out of the pRK5 vector. The subclone insert can undergo PCRto fuse in frame with a selected epitope tag such as a poly-his tag intoa Baculovirus expression vector. The poly-his tagged TAT insert can thenbe subcloned into a SV40 driven vector containing a selection markersuch as DHFR for selection of stable clones. Finally, the CHO cells canbe transfected (as described above) with the SV40 driven vector.Labeling may be performed, as described above, to verify expression. Theculture medium containing the expressed poly-His tagged TAT can then beconcentrated and purified by any selected method, such as byNi²⁺-chelate affinity chromatography.

TAT may also be expressed in CHO and/or COS cells by a transientexpression procedure or in CHO cells by another stable expressionprocedure.

Stable expression in CHO cells is performed using the followingprocedure. The proteins are expressed as an IgG construct(immunoadhesin), in which the coding sequences for the soluble forms(e.g. extracellular domains) of the respective proteins are fused to anIgG1 constant region sequence containing the hinge, CH2 and CH2 domainsand/or is a poly-His tagged form.

Following PCR amplification, the respective DNAs are subcloned in a CHOexpression vector using standard techniques as described in Ausubel etal., Current Protocols of Molecular Biology, Unit 3.16, John Wiley andSons (1997). CHO expression vectors are constructed to have compatiblerestriction sites 5′ and 3′ of the DNA of interest to allow theconvenient shuttling of cDNA's. The vector used expression in CHO cellsis as described in Lucas et al., Nucl. Acids Res. 24:9 (1774-1779(1996), and uses the SV40 early promoter/enhancer to drive expression ofthe cDNA of interest and dihydrofolate reductase (DHFR). DHFR expressionpermits selection for stable maintenance of the plasmid followingtransfection.

Twelve micrograms of the desired plasmid DNA is introduced intoapproximately 10 million CHO cells using commercially availabletransfection reagents Superfect® (Quiagen), Dosper® or Fugene®(Boehringer Mannheim). The cells are grown as described in Lucas et al.,supra. Approximately 3×10⁷ cells are frozen in an ampule for furthergrowth and production as described below.

The ampules containing the plasmid DNA are thawed by placement intowater bath and mixed by vortexing. The contents are pipetted into acentrifuge tube containing 10 mLs of media and centrifuged at 1000 rpmfor 5 minutes. The supernatant is aspirated and the cells areresuspended in 10 mL of selective media (0.2 μm filtered PS20 with 5%0.2 μm diafiltered fetal bovine serum). The cells are then aliquotedinto a 100 mL spinner containing 90 mL of selective media. After 1-2days, the cells are transferred into a 250 mL spinner filled with 150 mLselective growth medium and incubated at 37° C. After another 2-3 days,250 mL, 500 mL and 2000 mL spinners are seeded with 3×10⁵ cells/mL. Thecell media is exchanged with fresh media by centrifugation andresuspension in production medium. Although any suitable CHO media maybe employed, a production medium described in U.S. Pat. No. 5,122,469,issued Jun. 16, 1992 may actually be used. A 3L production spinner isseeded at 1.2×10⁶ cells/mL. On day 0, the cell number pH ie determined.On day 1, the spinner is sampled and sparging with filtered air iscommenced. On day 2, the spinner is sampled, the temperature shifted to33° C., and 30 mL of 500 g/L glucose and 0.6 mL of 10% antifoam (e.g.,35% polydimethylsiloxane emulsion, Dow Corning 365 Medical GradeEmulsion) taken. Throughout the production, the pH is adjusted asnecessary to keep it at around 7.2. After 10 days, or until theviability dropped below 70%, the cell culture is harvested bycentrifugation and filtering through a 0.22 μm filter. The filtrate waseither stored at 4° C. or immediately loaded onto columns forpurification.

For the poly-His tagged constructs, the proteins are purified using aNi-NTA column (Qiagen). Before purification, imidazole is added to theconditioned media to a concentration of 5 mM. The conditioned media ispumped onto a 6 ml Ni-NTA column equilibrated in 20 mM Hepes, pH 7.4,buffer containing 0.3 M NaCl and 5 mM imidazole at a flow rate of 4-5ml/min. at 4° C. After loading, the column is washed with additionalequilibration buffer and the protein eluted with equilibration buffercontaining 0.25 M imidazole. The highly purified protein is subsequentlydesalted into a storage buffer containing 10 mM Hepes, 0.14 M NaCl and4% mannitol, pH 6.8, with a 25 ml G25 Superfine (Pharmacia) column andstored at −80° C.

Immunoadhesin (Fc-containing) constructs are purified from theconditioned media as follows. The conditioned medium is pumped onto a 5ml Protein A column (Pharmacia) which had been equilibrated in 20 mM Naphosphate buffer, pH 6.8. After loading, the column is washedextensively with equilibration buffer before elution with 100 mM citricacid, pH 3.5. The eluted protein is immediately neutralized bycollecting 1 ml fractions into tubes containing 275 μL of 1 M Trisbuffer, pH 9. The highly purified protein is subsequently desalted intostorage buffer as described above for the poly-His tagged proteins. Thehomogeneity is assessed by SDS polyacrylamide gels and by N-terminalamino acid sequencing by Edman degradation.

Certain of the TAT polypeptides disclosed herein have been successfullyexpressed and purified using this technique(s).

Example 7 Expression of TAT in Yeast

The following method describes recombinant expression of TAT in yeast.

First, yeast expression vectors are constructed for intracellularproduction or secretion of TAT from the ADH2/GAPDH promoter. DNAencoding TAT and the promoter is inserted into suitable restrictionenzyme sites in the selected plasmid to direct intracellular expressionof TAT. For secretion, DNA encoding TAT can be cloned into the selectedplasmid, together with DNA encoding the ADH2/GAPDH promoter, a nativeTAT signal peptide or other mammalian signal peptide, or, for example, ayeast alpha-factor or invertase secretory signal/leader sequence, andlinker sequences (if needed) for expression of TAT.

Yeast cells, such as yeast strain AB110, can then be transformed withthe expression plasmids described above and cultured in selectedfermentation media. The transformed yeast supernatants can be analyzedby precipitation with 10% trichloroacetic acid and separation bySDS-PAGE, followed by staining of the gels with Coomassie Blue stain.

Recombinant TAT can subsequently be isolated and purified by removingthe yeast cells from the fermentation medium by centrifugation and thenconcentrating the medium using selected cartridge filters. Theconcentrate containing TAT may further be purified using selected columnchromatography resins.

Certain of the TAT polypeptides disclosed herein have been successfullyexpressed and purified using this technique(s).

Example 8 Expression of TAT in Baculovirus-Infected Insect Cells

The following method describes recombinant expression of TAT inBaculovirus-infected insect cells.

The sequence coding for TAT is fused upstream of an epitope tagcontained within a baculovirus expression vector. Such epitope tagsinclude poly-his tags and immunoglobulin tags (like Fc regions of IgG).A variety of plasmids may be employed, including plasmids derived fromcommercially available plasmids such as pVL1393 (Novagen). Briefly, thesequence encoding TAT or the desired portion of the coding sequence ofTAT such as the sequence encoding an extracellular domain of atransmembrane protein or the sequence encoding the mature protein if theprotein is extracellular is amplified by PCR with primers complementaryto the 5′ and 3′ regions. The 5′ primer may incorporate flanking(selected) restriction enzyme sites. The product is then digested withthose selected restriction enzymes and subcloned into the expressionvector.

Recombinant baculovirus is generated by co-transfecting the aboveplasmid and BaculoGold™ virus DNA (Pharmingen) into Spodopterafrugiperda (“Sf9”) cells (ATCC CRL 1711) using lipofectin (commerciallyavailable from GIBCO-BRL). After 4-5 days of incubation at 28° C., thereleased viruses are harvested and used for further amplifications.Viral infection and protein expression are performed as described byO'Reilley et al., Baculovirus expression vectors: A Laboratory Manual,Oxford: Oxford University Press (1994).

Expressed poly-his tagged TAT can then be purified, for example, byNi²⁺-chelate affinity chromatography as follows. Extracts are preparedfrom recombinant virus-infected Sf9 cells as described by Rupert et al.,Nature, 362:175-179 (1993). Briefly, Sf9 cells are washed, resuspendedin sonication buffer (25 mL Hepes, pH 7.9; 12.5 mM MgCl₂; 0.1 mM EDTA;10% glycerol; 0.1% NP-40; 0.4 M KCl), and sonicated twice for 20 secondson ice. The sonicates are cleared by centrifugation, and the supernatantis diluted 50-fold in loading buffer (50 mM phosphate, 300 mM NaCl, 10%glycerol, pH 7.8) and filtered through a 0.45 μm filter. A Ni²⁺-NTAagarose column (commercially available from Qiagen) is prepared with abed volume of 5 mL, washed with 25 mL of water and equilibrated with 25mL of loading buffer. The filtered cell extract is loaded onto thecolumn at 0.5 mL per minute. The column is washed to baseline A₂₈₀ withloading buffer, at which point fraction collection is started. Next, thecolumn is washed with a secondary wash buffer (50 mM phosphate; 300 mMNaCl, 10% glycerol, pH 6.0), which elutes nonspecifically bound protein.After reaching A₂₈₀ baseline again, the column is developed with a 0 to500 mM Imidazole gradient in the secondary wash buffer. One mL fractionsare collected and analyzed by SDS-PAGE and silver staining or Westernblot with Ni²⁺-NTA-conjugated to alkaline phosphatase (Qiagen).Fractions containing the eluted His₁₀-tagged TAT are pooled and dialyzedagainst loading buffer.

Alternatively, purification of the IgG tagged (or Fc tagged) TAT can beperformed using known chromatography techniques, including for instance,Protein A or protein G column chromatography.

Certain of the TAT polypeptides disclosed herein have been successfullyexpressed and purified using this technique(s).

Example 9 Preparation of Antibodies that Bind TAT

This example illustrates preparation of monoclonal antibodies which canspecifically bind TAT.

Techniques for producing the monoclonal antibodies are known in the artand are described, for instance, in Goding, supra. Immunogens that maybe employed include purified TAT, fusion proteins containing TAT, andcells expressing recombinant TAT on the cell surface. Selection of theimmunogen can be made by the skilled artisan without undueexperimentation.

Mice, such as Balb/c, are immunized with the TAT immunogen emulsified incomplete Freund's adjuvant and injected subcutaneously orintraperitoneally in an amount from 1-100 micrograms. Alternatively, theimmunogen is emulsified in MPL-TDM adjuvant (Ribi ImmunochemicalResearch, Hamilton, Mont.) and injected into the animal's hind footpads. The immunized mice are then boosted 10 to 12 days later withadditional immunogen emulsified in the selected adjuvant. Thereafter,for several weeks, the mice may also be boosted with additionalimmunization injections. Serum samples may be periodically obtained fromthe mice by retro-orbital bleeding for testing in ELISA assays to detectanti-TAT antibodies.

After a suitable antibody titer has been detected, the animals“positive” for antibodies can be injected with a final intravenousinjection of TAT. Three to four days later, the mice are sacrificed andthe spleen cells are harvested. The spleen cells are then fused (using35% polyethylene glycol) to a selected murine myeloma cell line such asP3X63AgU.1, available from ATCC, No. CRL 1597. The fusions generatehybridoma cells which can then be plated in 96 well tissue cultureplates containing HAT (hypoxanthine, aminopterin, and thymidine) mediumto inhibit proliferation of non-fused cells, myeloma hybrids, and spleencell hybrids.

The hybridoma cells will be screened in an ELISA for reactivity againstTAT. Determination of “positive” hybridoma cells secreting the desiredmonoclonal antibodies against TAT is within the skill in the art.

The positive hybridoma cells can be injected intraperitoneally intosyngeneic Balb/c mice to produce ascites containing the anti-TATmonoclonal antibodies. Alternatively, the hybridoma cells can be grownin tissue culture flasks or roller bottles. Purification of themonoclonal antibodies produced in the ascites can be accomplished usingammonium sulfate precipitation, followed by gel exclusionchromatography. Alternatively, affinity chromatography based uponbinding of antibody to protein A or protein G can be employed.

Antibodies directed against certain of the TAT polypeptides disclosedherein have been successfully produced using this technique(s).

Example 10 Purification of TAT Polypeptides Using Specific Antibodies

Native or recombinant TAT polypeptides may be purified by a variety ofstandard techniques in the art of protein purification. For example,pro-TAT polypeptide, mature TAT polypeptide, or pre-TAT polypeptide ispurified by immunoaffinity chromatography using antibodies specific forthe TAT polypeptide of interest. In general, an immunoaffinity column isconstructed by covalently coupling the anti-TAT polypeptide antibody toan activated chromatographic resin.

Polyclonal immunoglobulins are prepared from immune sera either byprecipitation with ammonium sulfate or by purification on immobilizedProtein A (Pharmacia LKB Biotechnology, Piscataway, N.J.). Likewise,monoclonal antibodies are prepared from mouse ascites fluid by ammoniumsulfate precipitation or chromatography on immobilized Protein A.Partially purified immunoglobulin is covalently attached to achromatographic resin such as CnBr-activated SEPHAROSE™ (Pharmacia LKBBiotechnology). The antibody is coupled to the resin, the resin isblocked, and the derivative resin is washed according to themanufacturer's instructions.

Such an immunoaffinity column is utilized in the purification of TATpolypeptide by preparing a fraction from cells containing TATpolypeptide in a soluble form. This preparation is derived bysolubilization of the whole cell or of a subcellular fraction obtainedvia differential centrifugation by the addition of detergent or by othermethods well known in the art. Alternatively, soluble TAT polypeptidecontaining a signal sequence may be secreted in useful quantity into themedium in which the cells are grown.

A soluble TAT polypeptide-containing preparation is passed over theimmunoaffinity column, and the column is washed under conditions thatallow the preferential absorbance of TAT polypeptide (e.g., high ionicstrength buffers in the presence of detergent). Then, the column iseluted under conditions that disrupt antibody/TAT polypeptide binding(e.g., a low pH buffer such as approximately pH 2-3, or a highconcentration of a chaotrope such as urea or thiocyanate ion), and TATpolypeptide is collected.

Deposit of Material

The following materials have been deposited with the American TypeCulture Collection, 10801 University Blvd., Manassas, Va. 20110-2209,USA (ATCC):

TABLE 7 Material ATCC Dep. No. Deposit Date DNA45234-1277 209654 Mar. 5,1998 DNA37151-1193 209393 Oct. 17, 1997

These deposits were made under the provisions of the Budapest Treaty onthe International Recognition of the Deposit of Microorganisms for thePurpose of Patent Procedure and the Regulations thereunder (BudapestTreaty). This assures maintenance of a viable culture of the deposit for30 years from the date of deposit. The deposits will be made availableby ATCC under the terms of the Budapest Treaty, and subject to anagreement between Genentech, Inc. and ATCC, which assures permanent andunrestricted availability of the progeny of the culture of the depositto the public upon issuance of the pertinent U.S. patent or upon layingopen to the public of any U.S. or foreign patent application, whichevercomes first, and assures availability of the progeny to one determinedby the U.S. Commissioner of Patents and Trademarks to be entitledthereto according to 35 USC § 122 and the Commissioner's rules pursuantthereto (including 37 CFR § 1.14 with particular reference to 886 OG638).

The assignee of the present application has agreed that if a culture ofthe materials on deposit should die or be lost or destroyed whencultivated under suitable conditions, the materials will be promptlyreplaced on notification with another of the same. Availability of thedeposited material is not to be construed as a license to practice theinvention in contravention of the rights granted under the authority ofany government in accordance with its patent laws.

The foregoing written specification is considered to be sufficient toenable one skilled in the art to practice the invention. The presentinvention is not to be limited in scope by the construct deposited,since the deposited embodiment is intended as a single illustration ofcertain aspects of the invention and any constructs that arefunctionally equivalent are within the scope of this invention. Thedeposit of material herein does not constitute an admission that thewritten description herein contained is inadequate to enable thepractice of any aspect of the invention, including the best modethereof, nor is it to be construed as limiting the scope of the claimsto the specific illustrations that it represents. Indeed, variousmodifications of the invention in addition to those shown and describedherein will become apparent to those skilled in the art from theforegoing description and fall within the scope of the appended claims.

1. An isolated polypeptide having at least 80% amino acid sequenceidentity to the amino acid sequence shown as SEQ ID NO:3.
 2. Theisolated polypeptide of claim 1 comprising the amino acid sequence shownas SEQ ID NO:3.
 3. A chimeric polypeptide comprising the polypeptide ofclaim 1 fused to a heterologous polypeptide.
 4. The chimeric polypeptideof claim 3, wherein said heterologous polypeptide is an epitope tagsequence or an Fc region of an immunoglobulin.